# Illumina Knowledge
Illumina Knowledge is a repository of 1634 FAQs, troubleshooting articles and reference material for Illumina products and workflows, covering all Illumina Microarrays and every stage of Sequencing. Use the navigation bar on the left of the page to find areas of interest and content types, use the search function at the top to query keywords. ## [What's New](/whats_new) * [QC for IDATs uploaded from an iScan to Illumina BioInsight Platform Core for Microarray Analysis](/microarray/general/microarray-general-reference_material-list/000010003) (*August 3, 2026*) | | | | :-: | ----------------------: | | | [*More...*](/whats_new) | ## [Announcements](/announcements) * Check out our NEW resource for [End-to-end sequencing and microarray training at Illumina Solutions Centers in the Americas](/instrumentation/general/instrumentation-general-reference_material-list/000008977). (*May 31, 2024*) | | | | :-: | --------------------------: | | | [*More...*](/announcements) | ## [Cloud Status](https://github.com/illumina-swi/illumina-knowledge/tree/master/docs/CLOUD_STATUS.md) * Click the link above to check on the status of Illumina cloud software products. # What's New Articles published to Illumina Knowledge in the past 2 months: * [QC for IDATs uploaded from an iScan to Illumina BioInsight Platform Core for Microarray Analysis](/microarray/general/microarray-general-reference_material-list/000010003) (*August 3, 2026*) * [0.8X bead cleanup to remove adapter dimers from Illumina Single Cell 3’ RNA Prep libraries](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009534) (*July 17, 2026*) * [AmpliSeq Antimicrobial Resistance Research Panel product, support, and manifest page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005186) (*July 17, 2026*) * [AmpliSeq Inborn Errors of Metabolism Research Panel v2 product, support, and manifest page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005198) (*July 17, 2026*) * [AmpliSeq On Demand Panel Product and Support Pages](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005535) (*July 17, 2026*) * [AmpliSeq for Illumina Autism Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005187) (*July 17, 2026*) * [AmpliSeq for Illumina BRCA Panel product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005521) (*July 17, 2026*) * [AmpliSeq for Illumina BRCA Plus, Extended Hereditary Breast and Ovarian Research Panel page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005188) (*July 17, 2026*) * [AmpliSeq for Illumina Cancer Hotspot v2 Panel product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005522) (*July 17, 2026*) * [AmpliSeq for Illumina Cardiovascular Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005189) (*July 17, 2026*) * [AmpliSeq for Illumina Childhood Cancer Panel product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005523) (*July 17, 2026*) * [AmpliSeq for Illumina Colon and Lung Research Panel v2 product, support, and manifest page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005190) (*July 17, 2026*) * [AmpliSeq for Illumina Comprehensive Panel v3 product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005524) (*July 17, 2026*) * [AmpliSeq for Illumina Custom DNA Panels product and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005533) (*July 17, 2026*) * [AmpliSeq for Illumina Custom RNA Panels product and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005534) (*July 17, 2026*) * [AmpliSeq for Illumina Deafness Research Panel v2 product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005185) (*July 17, 2026*) * [AmpliSeq for Illumina Dementia Research Gene Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005191) (*July 17, 2026*) * [AmpliSeq for Illumina Dysmorphia Dysplasia Research Panel v2 product, support, & manifest page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005193) (*July 17, 2026*) * [AmpliSeq for Illumina Ebola Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005194) (*July 17, 2026*) * [AmpliSeq for Illumina Focus Panel product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005526) (*July 17, 2026*) * [AmpliSeq for Illumina Gastrointestinal Research Panel v2 product, support, and manifest page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005195) (*July 17, 2026*) * [AmpliSeq for Illumina Hearing Loss Research Panel v1 product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005196) (*July 17, 2026*) * [AmpliSeq for Illumina Hematology Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005197) (*July 17, 2026*) * [AmpliSeq for Illumina Immune Repertoire Panel Plus, TCR beta Panel product and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005527) (*July 17, 2026*) * [AmpliSeq for Illumina Immune Response Panel product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005528) (*July 17, 2026*) * [AmpliSeq for Illumina Inherited Cancer Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005199) (*July 17, 2026*) * [AmpliSeq for Illumina Introduction Support Webinar Video](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000008039) (*July 17, 2026*) * [AmpliSeq for Illumina Library Prep, Indexes, and Accessories product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005532) (*July 17, 2026*) * [AmpliSeq for Illumina Long Non Coding RNA Research Panel product, support, and manifest page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005200) (*July 17, 2026*) * [AmpliSeq for Illumina Myeloid Panel product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005529) (*July 17, 2026*) * [AmpliSeq for Illumina Neurological Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005201) (*July 17, 2026*) * [AmpliSeq for Illumina Noonan Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005202) (*July 17, 2026*) * [AmpliSeq for Illumina Ophthalmic Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005203) (*July 17, 2026*) * [AmpliSeq for Illumina Primary Immune Deficiency Research Panel v2 page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005204) (*July 17, 2026*) * [AmpliSeq for Illumina Pulmonary Research Panel v2 product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005205) (*July 17, 2026*) * [AmpliSeq for Illumina RNA Fusion Lung Cancer Research Panel product, support, & manifest page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005206) (*July 17, 2026*) * [AmpliSeq for Illumina RNA Inflammation Response Research Panel product, support, & manifest page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005207) (*July 17, 2026*) * [AmpliSeq for Illumina RNA MAPK Pathway Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005208) (*July 17, 2026*) * [AmpliSeq for Illumina RNA Stem Cell Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005209) (*July 17, 2026*) * [AmpliSeq for Illumina RNA WNT Signaling Pathway Research Panel page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005210) (*July 17, 2026*) * [AmpliSeq for Illumina Renal Research Panel v2 product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005211) (*July 17, 2026*) * [AmpliSeq for Illumina SARS CoV 2 Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005212) (*July 17, 2026*) * [AmpliSeq for Illumina TB Research Panel product page, support page, and manifest links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005213) (*July 17, 2026*) * [AmpliSeq for Illumina TCR beta SR Panel product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005530) (*July 17, 2026*) * [AmpliSeq for Illumina Transcriptome Panel product page and support page links](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-reference_material-list/000005531) (*July 17, 2026*) * [Analysis options FAQ for Illumina Rapid RNA Kits](/software/dragen/software-dragen-faq-list/000010217) (*July 17, 2026*) * [Assessing cDNA QC in Illumina Single Cell 3' RNA Prep](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009524) (*July 17, 2026*) * [Assessing library QC in Illumina Single Cell 3' RNA Prep](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009527) (*July 17, 2026*) * [Bead clean up ratios used in the Illumina 16S Metagenomic Sequencing Library Preparation protocol](/library-preparation/custom-third-party-library-prep/library-preparation-custom-third-party-library-prep-faq-list/000006127) (*July 17, 2026*) * [Bead types in Illumina library preparation kits](/library-preparation/general-library-prep/library-preparation-general-library-prep-reference_material-list/000003342) (*July 17, 2026*) * [Best Practices for Nuclei Isolation with alternative isolation protocols for Illumina Single Cell](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009451) (*July 17, 2026*) * [Best practices for cell preparation for Illumina Single Cell 3' RNA prep](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009437) (*July 17, 2026*) * [Best practices for maintaining the computer on a MiSeq](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000006708) (*July 17, 2026*) * [Best practices for pipette mixing PIPs and cells/nuclei in Illumina Single Cell 3' RNA Prep](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009709) (*July 17, 2026*) * [Best practices for using Illumina Single Cell Nuclei Isolation Kits for Illumina Single Cell kits](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009450) (*July 17, 2026*) * [Can Illumina RNA Prep with Enrichment library prep and enrichment reagents be purchased separately?](/library-preparation/rna-enrichment-based-library-prep/library-preparation-rna-enrichment-based-library-prep-faq-list/000006623) (*July 17, 2026*) * [Can MiSeq Reagents be stored at 80°C rather than 20°C?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000008114) (*July 17, 2026*) * [Can PhiX and denatured PhiX be stored and used again?](/library-preparation/accessory-products/library-preparation-accessory-products-faq-list/000005128) (*July 17, 2026*) * [Can Sequencing Analysis Viewer (SAV) be used with the MiSeq System to view primary analysis results?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000002601) (*July 17, 2026*) * [Can a MiSeq post run wash be performed every week instead of entering standby mode?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000006976) (*July 17, 2026*) * [Can a MiSeq v2 flow cell be used for sequencing with a MiSeq v3 reagent cartridge?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000002317) (*July 17, 2026*) * [Can an entire index be N padded in Miseq Reporter?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000003624) (*July 17, 2026*) * [Can an expired reagent cartridge be used for a MiSeq run?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000002254) (*July 17, 2026*) * [Can library preparation reagents be stored in a frost free freezer?](/library-preparation/general-library-prep/library-preparation-general-library-prep-faq-list/000005798) (*July 17, 2026*) * [Can vortexing damage cells/nuclei when generating emulsions in the Illumina Single Cell workflow?](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-faq-list/000009458) (*July 17, 2026*) * [Can wells in index plates be used more than once?](/library-preparation/index-kits/library-preparation-index-kits-faq-list/000005240) (*July 17, 2026*) * [Capture and wash best practices for Illumina RNA Prep with Enrichment (L) Tagmentation](/library-preparation/rna-enrichment-based-library-prep/library-preparation-rna-enrichment-based-library-prep-reference_material-list/000003311) (*July 17, 2026*) * [Cell input and volume loading recommendations for Illumina Single Cell 3' RNA Prep](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009473) (*July 17, 2026*) * [Chemistry and Imaging on NovaSeq 6000](/instrumentation/novaseq-6000/instrumentation-novaseq-6000-reference_material-list/000008435) (*July 17, 2026*) * [Chemistry and imaging on MiSeq](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000003757) (*July 17, 2026*) * [Cleaning agents specifications and applications for Tecan (LiHa and RoMa) parts](/microarray/tecan-iaps/microarray-tecan-iaps-faq-list/000007003) (*July 17, 2026*) * [Converting ng/µl to nM when calculating dsDNA library concentration](/library-preparation/general-library-prep/library-preparation-general-library-prep-reference_material-list/000001240) (*July 17, 2026*) * [Custom sequencing primers on the MiSeq](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000002414) (*July 17, 2026*) * [DRAGEN Analysis Pipelines FAQ for Illumina Rapid RNA Kits](/software/dragen/software-dragen-faq-list/000010218) (*July 17, 2026*) * [Denature and dilution FAQ for Illumina DNA PCR Free](/library-preparation/dna-library-prep/library-preparation-dna-library-prep-faq-list/000003444) (*July 17, 2026*) * [Do MiSeq Wash Tubes include an expiration date?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000009678) (*July 17, 2026*) * [Does MiSeq verify the number of cycles in a planned run against the cycles supported by the reagent kit?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000003094) (*July 17, 2026*) * [Double sided size selection and bead clean up](/library-preparation/general-library-prep/library-preparation-general-library-prep-reference_material-list/000006157) (*July 17, 2026*) * [Enabling run storage and analysis in BaseSpace for MiSeq runs](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000003618) (*July 17, 2026*) * [Enrichment probe design FAQ for Illumina Rapid RNA kits](/library-preparation/rna-enrichment-based-library-prep/library-preparation-rna-enrichment-based-library-prep-faq-list/000010211) (*July 17, 2026*) * [Extending cDNA storage time in Illumina Single Cell 3' RNA Prep](/library-preparation/illumina-single-cell/library-preparation-illumina-single-cell-reference_material-list/000009394) (*July 17, 2026*) * [Freeze thaw stability and shelf life of TSO500 family automation library preparation kits](/library-preparation/trusight-oncology-tumor-library-prep/library-preparation-trusight-oncology-tumor-library-prep-reference_material-list/000003794) (*July 17, 2026*) * [Freeze thaw stability of TruSight Oncology 500 (TSO500) ctDNA (v1 and v2) input and reagents](/library-preparation/trusight-oncology-tumor-library-prep/library-preparation-trusight-oncology-tumor-library-prep-reference_material-list/000002919) (*July 17, 2026*) * [Frequently asked questions about upgrading to MiSeq Control Software v4.0](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000005752) (*July 17, 2026*) * [Frequently asked questions for AmpliSeq for Illumina On Demand panels](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-faq-list/000001048) (*July 17, 2026*) * [General information regarding RNA samples in the TruSight Oncology 500 (TSO500) v1 and v2 workflows](/library-preparation/trusight-oncology-tumor-library-prep/library-preparation-trusight-oncology-tumor-library-prep-reference_material-list/000003171) (*July 17, 2026*) * [How Long Does the Flow Rate Check Take During the MiSeq Pre Run Checks?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000009127) (*July 17, 2026*) * [How many freeze thaw cycles can TruSight Tumor 15 (TST15) library preparation reagents undergo?](/library-preparation/trusight-oncology-tumor-library-prep/library-preparation-trusight-oncology-tumor-library-prep-faq-list/000008398) (*July 17, 2026*) * [How many reactions are in the AmpliSeq Library Equalizer for Illumina?](/library-preparation/ampliseq-library-prep/library-preparation-ampliseq-library-prep-faq-list/000006521) (*July 17, 2026*) * [How much template does the MiSeq System use?](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000002524) (*July 17, 2026*) * [How to Check if a MiSeq Reagent Cartridge was pierced during a run](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000003497) (*July 17, 2026*) * [How to Perform Washes on the MiSeq Video](/instrumentation/general/instrumentation-general-reference_material-list/000006958) (*July 17, 2026*) * [How to access MiSeq Reporter](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000003627) (*July 17, 2026*) * [How to access Windows on the MiSeq if there is black screen at boot up](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001658) (*July 17, 2026*) * [How to add an Administrator account to Windows 10 Operating System on the NovaSeq 6000](/instrumentation/novaseq-6000/instrumentation-novaseq-6000-reference_material-list/000007867) (*July 17, 2026*) * [How to change the date format in the GenomeStudio Final Report in the Processing Date Field](/microarray/human-genotyping/microarray-human-genotyping-reference_material-list/000005246) (*July 17, 2026*) * [How to check network settings on the MiSeq](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000002383) (*July 17, 2026*) * [How to clean the MiSeq flow cell holder](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000003500) (*July 17, 2026*) * [How to generate an RFID bypass code in MyIllumina Video](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000005859) (*July 17, 2026*) * [How to obtain Unmethylated and Methylated signal in GenomeStudio for each CpG in the Infinium MethylationEPIC Array](/microarray/non-human-methylation/microarray-non-human-methylation-troubleshooting-list/000006306) (*July 17, 2026*) * [How to stop a MiSeq run](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-faq-list/000005081) (*July 17, 2026*) * [How to upload a run to BaseSpace using BaseSpace Command Line Interface (CLI)](/software/basespace-cli/software-basespace-cli-reference_material-list/000003298) (*July 17, 2026*) * [Important file types for analysis of BeadArray data in BlueFuse Multi](/microarray/bluefuse-multi/microarray-bluefuse-multi-troubleshooting-list/000005043) (*July 17, 2026*) * [Infinium Assay Workflow for HD, HTS, and LCG (Non EX Formats) Support Video](/microarray/general/microarray-general-reference_material-list/000005791) (*July 17, 2026*) * [Troubleshooting "Access to the path 'Global\Local Run Manager' is denied" on MiSeq](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000008538) (*July 17, 2026*) * [Troubleshooting a bubble in MiSeq flow cell](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-troubleshooting-list/000001996) (*July 17, 2026*) * [Turnaround time, throughput, and workflow requirements for COVIDSeq (RUO)](/library-preparation/amplicon-library-prep/library-preparation-amplicon-library-prep-faq-list/000005436) (*July 17, 2026*) * [What Tecan/Illumina instrument and software combinations require the use of Tip Guides?](/microarray/tecan-iaps/microarray-tecan-iaps-faq-list/000009625) (*July 17, 2026*) * [What to do if a BaseSpace analysis is stuck or stalled running](/software/basespace-sequence-hub/software-basespace-sequence-hub-troubleshooting-list/000007380) (*July 17, 2026*) * [Infinium Methylation Screening Array Manifest Column Headings](/microarray/iscan/microarray-iscan-reference_material-list/000010058) (*July 16, 2026*) * [Consumables and Equipment FAQ for the TruPath Genome assay](/library-preparation/general/library-preparation-general-faq-list/000010166) (*July 15, 2026*) * [Frequently Asked Questions for Illumina FFPE DNA Prep with Exome 2.5 Enrichment](/library-preparation/general/library-preparation-general-faq-list/000009485) (*July 15, 2026*) * [General FAQ for Illumina Rapid RNA kits](/library-preparation/general/library-preparation-general-faq-list/000010209) (*July 15, 2026*) * [Input recommendations for Illumina Rapid RNA Kits](/library-preparation/general/library-preparation-general-faq-list/000010212) (*July 15, 2026*) * [Installing Reference Genomes on NovaSeq X Series Control Software v1.4](/instrumentation/general/instrumentation-general-reference_material-list/000010233) (*July 15, 2026*) * [Kits, consumables, and reagent stability FAQ for Illumina Rapid RNA Kits](/library-preparation/general/library-preparation-general-faq-list/000010210) (*July 15, 2026*) * [QC steps FAQ for Illumina Rapid RNA Kits](/library-preparation/general/library-preparation-general-faq-list/000010214) (*July 15, 2026*) * [Read Depth Requirements for Illumina Rapid RNA kits](/library-preparation/general/library-preparation-general-reference_material-list/000010216) (*July 15, 2026*) * [Resources for Illumina Rapid RNA kits](/library-preparation/general/library-preparation-general-reference_material-list/000010220) (*July 15, 2026*) * [Sequencing and run setup FAQ for Illumina Rapid RNA Kits](/library-preparation/general/library-preparation-general-faq-list/000010215) (*July 15, 2026*) * [Workflow FAQ for Illumina Rapid RNA Kits](/library-preparation/general/library-preparation-general-faq-list/000010213) (*July 15, 2026*) # Announcements * Check out our NEW resource for [End-to-end sequencing and microarray training at Illumina Solutions Centers in the Americas](/instrumentation/general/instrumentation-general-reference_material-list/000008977). (*May 31, 2024*) # Cloud Status # General # FAQ Instrumentation > General > FAQ * [Are the RFID tags for the flow cell and reagent cartridge linked?](/instrumentation/general/instrumentation-general-faq-list/000002528) * [Can secondary analysis run on MiSeq while a run is in progress?](/instrumentation/general/instrumentation-general-faq-list/000002604) * [Differences in the percent clusters passing filter on patterned and non patterned flow cells](/instrumentation/general/instrumentation-general-faq-list/000007457) * [How is PhiX alignment calculated by RTA (Real Time Analysis)?](/instrumentation/general/instrumentation-general-faq-list/000005576) * [How to Check When a Windows Password Was Last Updated or When It Will Expire](/instrumentation/general/instrumentation-general-faq-list/000003269) * [How to determine the appropriate kit configuration to use based on the data needed?](/instrumentation/general/instrumentation-general-faq-list/000006622) * [Illumina reagent shipment packaging FAQs](/instrumentation/general/instrumentation-general-faq-list/000008401) * [Is it possible to remove a library pool from a sequencing reagent cartridge?](/instrumentation/general/instrumentation-general-faq-list/000007771) * [Operating System (OS) versions on Illumina platforms](/instrumentation/general/instrumentation-general-faq-list/000006353) * [Procedures for cleaning flow cells for Illumina sequencers](/instrumentation/general/instrumentation-general-faq-list/000005147) * [Reagent Expiration Date Definition](/instrumentation/general/instrumentation-general-faq-list/000007148) * [Secure communication protocols on Illumina systems](/instrumentation/general/instrumentation-general-faq-list/000008965) * [Steps if insufficient wash solution was used in a manual wash on the NextSeq 500/550 or MiniSeq](/instrumentation/general/instrumentation-general-faq-list/000003047) * [What are Illumina's Qualification Service Offerings](/instrumentation/general/instrumentation-general-faq-list/000007027) * [What files are required to view a run in Sequencing Analysis Viewer (SAV)?](/instrumentation/general/instrumentation-general-faq-list/000003234) * [What is the difference between NextSeq PhiX Control Kit and PhiX Control v3?](/instrumentation/general/instrumentation-general-faq-list/000002925) * [What is the maximum Sample ID length?](/instrumentation/general/instrumentation-general-faq-list/000003631) * [Where to find the date of manufacture of Illumina instruments?](/instrumentation/general/instrumentation-general-faq-list/000008548) * [Which sequencers use patterned vs. nonpatterned flow cells?](/instrumentation/general/instrumentation-general-faq-list/000007786) * [Windows 10 Upgrade for Illumina Instruments FAQ](/instrumentation/general/instrumentation-general-faq-list/000002247) # Are the RFID tags for the flow cell and reagent cartridge linked? The RFID tags for the flow cell and reagent cartridge are not linked. The flow cell RFID is unique to the flow cell and the reagent cartridge RFID is unique to the reagent cartridge. Each component in a reagent kit has its own RFID code that is read independently. **Note**: Illumina reagents are equipped with a radio-frequency identification (RFID) tag to enable accurate consumable tracking. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2528), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002528%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Can secondary analysis run on MiSeq while a run is in progress? It is **not possible** to perform secondary analysis on the MiSeq when a sequencing run is in progress. If a new sequencing run is started on the MiSeq before the secondary analysis of a previous run is complete, the secondary analysis is stopped automatically. MiSeq computing resources are dedicated to either sequencing or analysis, and the system is designed in such a way that a sequencing command overrides an analysis command. Secondary analysis can be requeued from MiSeq Reporter or Local Run Manager, when sequencing is not in progress. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2604), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002604%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Differences in the percent clusters passing filter on patterned and non patterned flow cells Illumina sequencers use either patterned or non-patterned flow cells. Instruments that usenon-patterned flow cells areMiSeq, NextSeq 500/550, and MiniSeq. Instruments that usepatterned flow cells include iSeq 100, NextSeq 1000/2000, NovaSeq 6000, NovaSeq X Series, and MiSeq i100 Series. Instruments that use patterned flow cells have artificially lower percent clusters Passing Filter (%PF) metrics compared to non-patterned flow cells. * With patterned flow cells, there is no template generation or preliminary filtration step during image analysis, which results in lower %PF values. * Because template generation and the associated preliminary filtration steps are not applied, all nanowells, including empty wells or clusters that may be dim, low quality, or polyclonal are included in the raw cluster count, which leads to lower %PF values. * The uniform feature sizes and optimal spacing in the patterned flow cell enable significantly increased cluster density for patterned flow cells, ultimately resulting in a greater yield capacity. * Although the %PF metric is generally lower with patterned flow cells, it does not negatively impact performance or data quality. * Consult the specifications for the instrument and sequencing configuration to evaluate run performance, quality, and data output. For further information, see Knowledge Base article [Calculating Percent Passing Filter for Patterned and Nonpatterned Flow Cells](/instrumentation/general/instrumentation-general-reference_material-list/000006309) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7457), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006309%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How is PhiX alignment calculated by RTA (Real Time Analysis)? The Real Time Analysis (RTA) software calculates the percentage of reads passing filter that align to the PhiX reference genome. PhiX alignment is calculated over the first 25 cycles of the insert reads. If there are >2 mismatches in the first 25 cycles, a read will not be called as PhiX. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5576), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005576%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Check When a Windows Password Was Last Updated or When It Will Expire ### **Overview** If experiencing issues related to login credentials or service authentication, checking the password history and expiration date for Windows accounts can help identify the root cause. This is especially useful when working with benchtop instruments or software like Local Run Manager (LRM). ### **Steps to Check Password Info** **1. Open Command Prompt** Search for "cmd" in the Windows Search box to open Windows **Command Prompt** **2. Run the Following Commands** Enter each command into the Command Prompt, select **Enter** after each entry: * * `net user sbsuser` * net user sbsadmin These commands display account details, including: * * Password last set date * Password expires * Account active status **3. Review or Share the Results** Take a screenshot of the output to share with Illumina Technical Support as needed. ![](/files/7RP92oWlvKX4ziSFIJuJ) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #3269), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003269%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to determine the appropriate kit configuration to use based on the data needed? To determine the number of reads needed for the run (project), multiply the desired reads per sample by the number of samples in the pool. With the total number of reads, identify the kit and sequencer that fits the data needs using the sequencer specifications pages, listed below. * [Specifications for the iSeq 100 System](https://www.illumina.com/systems/sequencing-platforms/iseq/specifications.html) * [Specifications for the MiniSeq System](https://www.illumina.com/systems/sequencing-platforms/miniseq/specifications.html) * [Specifications for the MiSeq System](https://www.illumina.com/systems/sequencing-platforms/miseq/specifications.html) * [Specifications for the NextSeq 500/550 System](https://www.illumina.com/systems/sequencing-platforms/nextseq/specifications.html) * [Specifications for the NextSeq 1000/2000 System](https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000/specifications.html) * [Specifications for the HiSeq 3000/4000 System](https://www.illumina.com/systems/sequencing-platforms/hiseq-3000-4000/specifications.html) * [Specifications for the NovaSeq 6000 System](https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html) * [Specifications for the NovaSeq X/X Plus](https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6622), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006622%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Illumina reagent shipment packaging FAQs **Why are there different amounts of dry ice in different shipments?**\ Depending on the temperatures that the shipment encounters in transit, there may be differences in the amounts of dry ice left in containers upon delivery. If there is any dry ice left in the container, then the product is good to use. Dry ice quantities have been optimized for ideal product quality in transit. Illumina continues to work on reducing environmental impact and improving customer experience. **Gel packs are not fully frozen. Is this an issue?**\ Gel packs have been validated to maintain temperature for transit durations based on historical data and may not be frozen upon delivery. For any specific concerns or questions about the integrity of the product(s) ordered, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support). **Illumina frozen product boxes are tearing when separating them. Is this a risk to the product?**\ Boxes may freeze together because of condensation and extreme cold due to dry ice. This damage occurs when the boxes are separated immediately after removing from contact with dry ice, is cosmetic only, and does not affect product performance. Letting the boxes sit out at room temperature for approximately 5 minutes after removal from insulated containers will allow them to separate without cosmetic damage. **Why are some shipping containers wet?**\ Condensation on the shipping containers is due to extreme temperature differences between the dry ice and product inside the insulated container during hot and/or humid weather conditions. Shipping containers have passed rigorous thermal and simulated distribution testing, and condensation does not affect the products inside. **My product came shipped at a different temperature than the storage temperature. Is the product okay?**\ To minimize Illumina's environmental footprint and provide an efficient unpacking experience, some products are tested to be able to ship at different temperatures than their recommended storage conditions. Always check the product label for the appropriate storage condition of your products upon receipt. These products have passed rigorous testing and evaluation for product quality throughout Illumina’s global supply chain. **What are the foil/silver bags in dry ice shipments?**\ To minimize condensation, Illumina has implemented metallized bags inside of some longer-duration shipments. **How should shipping containers and insulation be disposed?**\ Refer to the shipping box graphics to determine how to best dispose of (or return) specific shipping containers and insulation. If no instructions are given, boxes can be disposed of through the waste stream. **Why do some shipments include both foam containers and sustainable containers?**\ Shipping container selection depends on the site shipping the product and the availability of locally sourced materials. Illumina continues to increase the percentage of sustainable insulated containers as Illumina is committed to reducing environmental impact. See the [Illumina annual Corporate Social Responsibility (CSR) report](https://www.illumina.com/company/about-us/corporate-social-responsibility.html) for more information. **The packaging is damaged. Is a replacement product required?**\ Most packaging damages are minor and do not pose a risk to the product. Outer packaging has been designed to take on impact to protect the product inside.\ For specific concerns or questions about the integrity of the product(s) ordered, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support).\ Examples of acceptable conditions include: * Reduced quantity of dry ice is present with frost still visible. ![](/files/knGts8ecoVk1SdTzwZjG)\ ![](/files/xbGWV1RS8EB5WKTr6nDD) * External minor damage to insulated container with no impact to product or any other contents. ![](/files/0PDs03UFO8b6lj9AwV6c)\ ![](/files/Wo6BAWA8syh03qd6ctEG) * Creasing on box, surface tears or minor punctures that do not affect readability of label or integrity of box. ![](/files/oftWD4LyNT3NUG4OJnmA)\ ![](/files/7pqrpY6MyRYProvbEGNf) * Box edges slightly bent with creases or tears but integrity of box not impaired. ![](/files/tV3Gh8mvvAVGzrmXtbg6) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8401), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008401%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Is it possible to remove a library pool from a sequencing reagent cartridge? **If a library pool has already been loaded into a sequencing reagent cartridge, is it possible to remove the library and re-use the reagent kit with the same or a different library pool (if sequencing has not been performed)?** Generally, once the library is loaded into a reagent cartridge, Illumina does not recommend removing the library pool. If sequencing is significantly delayed after loading a library pool, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) for additional information. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7771), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007771%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Operating System (OS) versions on Illumina platforms **Background** Each Illumina platform has either a Windows or Linux OS environment that the Control Software will run in. The following lists available Illumina platforms and the associated OS version according to instrument platform or Control Software version, where applicable. All current versions of the Windows and Linux OS on Illumina platforms use the Long Term Support (LTS) versions which have extended service lifecycles. *Illumina Sequencing Platforms* * **iSeq 100 platform**: Windows 10 Enterprise 2016 LTSB, Version 1607 * **MiniSeq MnCS v2.x**: Windows 10 Enterprise 2019 LTSC, Version 1809 * **MiSeq MCS v4.x**: Windows 10 Enterprise 2019 LTSC, Version 1809 * **NextSeq 500/550 NCS v4.x**: Windows 10 Enterprise 2019 LTSC, Version 1809\* * **NovaSeq 6000, Model 30.0.C06.########:** Windows 10 Enterprise 2016 LTSB, Version 1607\* * **NovaSeq 6000, Model 30.1.C01.########:** Windows 10 Enterprise 2019 LTSC, Version 1809\* * **NextSeq 1000/2000 platforms**: Linux CentOS 7 * **Note:** NextSeq 1000/2000 Control Software v2.0.0 has the Oracle 9 Linux operating system. * **NovaSeq X Series**: * SBC: Oracle Linux Server 8\ \- Kernel: 4.18.0-425.13.1.el8\_7.x86\_64 * CE/COMe: Oracle Linux 8\ \- Kernel: 4.18.0-372.32.1.0.1.el8\_6.x86\_64 * **MiSeq i100 Series**: * CE/COMe: Oracle Linux Server 9\ \- Kernel: 5.14.0-427.13.1.el9\_4.x86\_64 *Illumina Array Platforms* * **iScan Platforms**\*\* * A8202 Supporting PC: Windows 10 Enterprise 2016 LTSB, Version 1607 * **Tecan Platforms** * Illumina Automation Control (IAC): Windows 10 Enterprise 2019 LTSC, Version 1809 (32-bit) * **Tecan/Hamilton Platforms**: Windows 10 Enterprise 2019 LTSC, Version 1809 \* For the NextSeq 500/550 and NovaSeq 6000, the Windows 10 LTS version depends on the the manufacturing date and current Software image. Use the following steps to confirm the Windows OS version. 1. From the Windows Start menu, select **Settings**. 2. In the Settings window, select **System** and then select **About** in the menu on the left. 3. The Windows OS version is listed under **Windows specifications** header. 1. The model number, if applicable, is listed under the **Device specifications**. \*\* For the iScan platform, the Windows OS version will depend on the Supporting PC version that is supplied with the iScan instrument. To determine the version, check the white label sticker on the side of the Supporting PC. Please see [Windows 10 support and timelines for Illumina sequencing and array instrument computers](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Windows-10-support-and-timelines-for-Illumina-sequencing-and-array-instrument-computers/README.md) for more information. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6353), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009668%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Procedures for cleaning flow cells for Illumina sequencers **iSeq 100** * No cleaning required. * Only touch the plastic when handling the flow cell. * Avoid touching the electrical interface, CMOS sensor, glass, and gaskets on either side of the glass. * Reference: [iSeq 100 Sequencing System Product Documentation](https://support.illumina.com/downloads/iseq-100-system-guide.html). ![](/files/xZmEnrpfKNtpH4tLV8f7) **MiniSeq** * Put on a new pair of powder-free gloves. * Remove the flow cell from the container. * Clean the glass surface of the flow cell with a lint-free alcohol wipe. * Dry with a lint-free lens cleaning tissue. Use care around the black flow cell gasket. * Inspect the flow cell port for obstructions. Make sure that the gasket is well-seated. * Reference: [MiniSeq System Guide](https://support.illumina.com/downloads/miniseq-system-guide-1000000002695.html). ![](/files/yJntnIq71VP5Ae9WqO9A) **MiSeq** * Put on a new pair of powder-free gloves. * Remove the flow cell from the container. * Lightly rinse the flow cell with laboratory grade water until both the glass and the plastic cartridge are thoroughly rinsed of excess salts. * Using care around the black flow cell port gasket, thoroughly dry the flow cell glass and plastic with a lint-free lens cleaning tissue. Gently pat dry in the area of the gasket and adjacent glass. * Clean the flow cell glass with an alcohol wipe. Make sure that the glass is free of streaks, fingerprints, and lint or tissue fibres. * **DO NOT USE THE ALCOHOL WIPE ON THE FLOW CELL PORT GASKET.** * Dry excess alcohol with a lint-free lens cleaning tissue. * Inspect the flow cell port for obstructions. Make sure that the gasket is well-seated. If the gasket appears to be dislodged, gently press it back until it sits securely around the flow cell ports. * Reference: [MiSeq System Guide for Windows 10](https://support.illumina.com/downloads/miseq_system_user_guide_15027617.html) and [MiSeq System Guide for Windows 7](https://support.illumina.com/downloads/miseq_system_user_guide_win7.html). ![](/files/j3G2E5D2spQ7KuKMoeCc) **NextSeq 500/550** * Remove the flow cell from the foil packaging. * Open the clear plastic clamshell package and remove the flow cell. * Clean the glass surface of the flow cell with a lint-free alcohol wipe. Dry the glass with a low-lint lab tissue. * Reference: [NextSeq 500 and NextSeq 550 Sequencing System Guide](https://support.illumina.com/downloads/nextseq-500-550-systems-product-documentation.html) ![](/files/d9pgNtoUfSimJlVSvbST) **NextSeq 1000/2000** * The flow cell **MUST NOT** be cleaned. * Flow cells can look streaky; they are fine to use. * Reference [NextSeq 1000/2000 Product Documentation](https://support.illumina.com/downloads/nextseq-1000-2000-product-documentation-200027171.html). ![](/files/DsTI1qR2bfL3zq7EAiuK) **NovaSeq 6000** * It is not necessary to clean the flow cell. * If desired, clean the glass surface of the flow cell with a lint-free alcohol wipe. Dry the glass with a low-lint lab tissue. * Reference: [NovaSeq 6000 Sequencing System Guide](https://support.illumina.com/downloads/novaseq-6000-system-guide-1000000019358.html). ![](/files/wxZFz9B7SA0FcyKIM2nU) **NovaSeq X Series** * Put on a new pair of powder-free gloves to avoid contaminating the glass surface of the flow cell. * With the flow cell foil package over a flat surface, peel open the foil from the corner tab * Remove the flow cell from the package. Grasp the flow cell by the sides to avoid touching the glass or the underside gaskets. * **Always** clean the flow cell, whether or not a contaminant is present, using the following steps: 1. Wet a Contec Polynit Heatseal wipe with isopropyl alcohol (70%). 2. Gently clean the applicable surface. Wipe in a lengthwise direction (top to bottom direction) only, avoiding gaskets and manifolds. 3. Repeat steps **a** and **b** until surfaces are clear. 4. Dry with a new polynit heatseal wipe or an unused side of the used wipe to avoid contamination. * Do NOT use other lint-free wipes such as Kim Wipes or similar products. Only use Contec Polynit Heatseal wipes. * Always use isopropyl alcohol over ethanol due to higher purity. * Reference: [NovaSeq X Series](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/FrontPages/NovaSeqX.htm). ![](/files/fNmFJfql8zRfr6zpEaV6) **MiSeq i100** * No cleaning required (CMOS patterned flow cell integrated into the Dry cartridge). * Cartridge should be gripped from the side to avoid touching the flowcell circuit/CMOS sensor. * Reference: [MiSeq i100 Plus System](https://support-docs.illumina.com/IN/MiSeqi100Series/Content/IN/FrontPages/MiSeqi100.htm). ![](/files/6EwsSGBdPurE8yKnS9Dt) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5147), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005147%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Reagent Expiration Date Definition The control software for all instruments will allow the reagents to be used **the day of expiration** thus they are still within their expiration until the end of that day. For example: If the expiration date states 25-Oct-2022, the reagents are within Illumina's consumable warranty if used on 25-Oct-2022 and can be used until 26-Oct-2022. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7148), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007148%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Secure communication protocols on Illumina systems **What is a communication protocol, in simple terms?** When data is transferred from Illumina sequencers and servers to a user network storage location, there are different levels of Server Message Block (SMB) protocols that can be employed. **What are the latest secure communication protocols supported on Illumina instruments?** All Windows 10 systems support SMB 3.1.1 The NextSeq 1000/2000 (CentOS 7) supports SMB 3.0 The NovaSeq X/X Plus (Oracle Linux 8) supports SMB 3.1.1 \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8965), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008965%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Steps if insufficient wash solution was used in a manual wash on the NextSeq 500/550 or MiniSeq If there is not enough wash solution in the wash tray during a manual wash, this can introduce air into the system which can negatively impact subsequent sequencing run performance. To fix this, Illumina recommends performing 2-3 maintenance washes on the instrument to flush the fluidics lines and remove any air bubbles. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #3047), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003047%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # What are Illumina's Qualification Service Offerings Below is a comparison of Illumina's Qualification Service Offerings. More information can be found at [Illumina's Service Product site](https://www.illumina.com/products/by-type/service-products.html). [Installation Qualification (IQ)](https://www.illumina.com/products/by-type/service-products/installation-operational-qualification.html) Provides documented verification that the instrument is installed according to our specifications and safety regulations. During the IQ, a trained engineer confirms that the latest supported firmware and software versions were installed, verifies instrument setup and accessory logistics, checks that physical and environmental safety conditions are met, and provides a signed, audit-ready, digital document. [Operational Qualification (OQ)](https://www.illumina.com/products/by-type/service-products/operational-qualifications.html) Follows a comprehensive, well-defined protocol to make sure that the system is functioning according to our preset and validated operational specifications. The OQ protocol was developed and validated in Illumina labs and is updated after each instrument hardware and software release, so you receive the most up-to-date service. Critical aspects of the OQ include motion, optics, fluidics, and thermal qualifications. [Performance Qualification (PQ)](https://www.illumina.com/products/by-type/service-products/performance-qualifications.html) Follows a comprehensive, well-defined protocol to make sure that the instrument is functioning according to our preset and validated performance specifications. The PQ protocol was developed and validated in Illumina labs and is updated after each instrument hardware and software release, so you receive the most up-to-date service. Critical aspects of the PQ include a PhiX data run (including projected yield total), data quality, and any additional comments.
Qualification ServiceQualification Recommended IntervalsEvent-Specific Service
Installation Qualification (IQ)
  • During initial installation
  • After relocation and reinstallation
  • Before first-time use
  • After general changes to lab environment (eg, remodeling, construction, electrical disruptions)
Operational Qualification (OQ)
  • During initial installation
  • After a reactive service, or software upgrade, or preventive maintenance
  • Periodically, according to lab standard operating procedure
  • With an IQ to test for baseline level of instrument performance
  • Before starting a major study or experiments
Performance Qualification (PQ)After any qualified major repairAfter maintenance, replacement, or upgrade of selected modules
\ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7027), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007027%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # What files are required to view a run in Sequencing Analysis Viewer (SAV)? The Sequencing Analysis Viewer (SAV) is a software application where users can view quality metrics generated during a sequencing run by Real-Time Analysis (RTA) software on Illumina sequencing systems. RTA is compatible with iSeq 100, MiSeq, MiSeq i100, MiniSeq, NextSeq 500/550, NextSeq 1000/2000, NovaSeq 6000, NovaSeq X Series, and the available Dx versions for some of these instruments. For viewing these metrics on SAV, the following is needed: * InterOp folder * RunInfo.xml * RunParameters.xml For specific details on where these files and folder are located on different Illumina sequencers, refer to one of the File Path articles listed below: * [iSeq 100](/instrumentation/iseq-100/instrumentation-iseq-100-reference_material-list/000002287) * [MiSeq](/instrumentation/miseq-ruo/instrumentation-miseq-ruo-reference_material-list/000001678) * [MiSeq i100](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/File-paths-on-the-MiSeq-i100-Series/README.md) * MiniSeq (for Control Software [v1.2](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/File-Paths-for-the-MiniSeq-Control-Software-1-2/README.md) or [v.2.0](/instrumentation/miniseq/instrumentation-miniseq-reference_material-list/000002378)) * [NextSeq 500/550](/instrumentation/nextseq-500-550/instrumentation-nextseq-500-550-reference_material-list/000002072) * [NextSeq 1000/2000](/instrumentation/nextseq-1000-2000/instrumentation-nextseq-1000-2000-reference_material-list/000002443) * [NovaSeq 6000](/instrumentation/novaseq-6000/instrumentation-novaseq-6000-reference_material-list/000002426) * [NovaSeq X Series](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/File-paths-on-the-NovaSeq-X/README.md) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #3234), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007515%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # What is the difference between NextSeq PhiX Control Kit and PhiX Control v3? * The PhiX library is the same in both kits, thus either kit can be used in any Illumina sequencing platforms. * The only difference between kits is that the ***NextSeq PhiX Control Kit*** also includes Resuspension Buffer (RSB) whereas the ***PhiX Control v3*** does not. | Part Name | Part Number | Includes RSB? | | ------------------------ | -------------------------------- | ------------- | | NextSeq PhiX Control Kit |

15051973
(FC-110-3002)

| Yes | | PhiX Control v3 |

15017872
(FC-110-3001)

| No | \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2925), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002925%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # What is the maximum Sample ID length? When creating SampleSheets, the Sample ID field is used to identify samples, and to name the FASTQ files generated. The Sample ID field can contain alphanumeric characters, hyphens and underscores, with maximum lengths depending on the software used for Sample Sheet creation and analysis: -BaseSpace Run Planning: Maximum of 100 characters. -Local Run Manager v3: Maximum of 40 characters\*. -Local Run Manager v4: Maximum of 90 characters\*. **\*NOTE:** Local Run Manager will not allow for hyphens and underscores to be at the end of the Sample ID, they need to be in the middle. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #3631), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003631%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Where to find the date of manufacture of Illumina instruments? The country of origin and date of manufacture of Illumina instruments are printed on the label placed on the back of the instrument. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8548), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008548%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Which sequencers use patterned vs. nonpatterned flow cells? Patterned flow cells consist of a nanowell substrate with billions of ordered wells. Compared to nonpatterned flow cells, the uniform cluster sizes enable optimal spacing and increased cluster density. See Knowledge Article **Calculating Percent Passing Filter for Patterned and Nonpatterned Flow Cells** for more information. Instruments that use **patterned flow cells**: NovaSeq 6000, NovaSeq X/X Plus, NextSeq 1000/2000, MiSeq i100, iSeq 100, HiSeq 3000/4000/X. Instruments that use **non-patterned flow cells**: MiSeq, NextSeq 500/550, MiniSeq, HiSeq 1000/1500/2000/2500. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7786), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007786%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Windows 10 Upgrade for Illumina Instruments FAQ 1- Is there any preparation required for the upgrade? A: We recommend that users inform their organization's IT team regarding the upgrade to ensure rapid connection back to their network. A pre-upgrade checklist will be provided when the upgrade is scheduled. 2. Is there a way to check whether my instrument is on Windows 7 Professional or Windows 7 Embedded? A: In the Windows 7 operating system, go to Control Panel > All Control Panel Items > System. Windows edition will show as Windows 7 Professional or Windows 7 Embedded. 3. Where are the Extended Security Update (ESU) licenses for Windows 7 Professional available? A: See our[Prerequisites for ESU Licenses for Windows 7 Professional](https://support.illumina.com/support-content/windows10/win7-esu-prerequisites.html) page for more details. 4. Will there be any impact on the instrument if it stays on Windows 7? A: While instruments will continue to function normally, we encourage the upgrade to Windows 10. Using an unsupported operating system increases the risk of exposure to malware. If users choose to remain on Windows 7, they should take appropriate steps to minimize exposure. 5. Who is responsible for upgrading the instrument? A: When ready to upgrade an instrument, reach out to Illumina Technical Support or to your local field team to schedule a visit from an Illumina Field Service Engineer who will perform the upgrade. 6. Can I upgrade the instrument on my own? A: No, the upgrade requires a visit from an Illumina Field Service Engineer. 7. Is there a cost to upgrade an instrument under a service contract? A: No. Instruments under an active service contract of any tier will have their upgrade covered. 8. What is the cost to upgrade an instrument that is not under a service contract? A: The cost will vary per instrument. Reach out to Illumina Technical Support or your local field team to request a quote. **NOTE:** Microsoft has announced that standard retail versions of Windows 10 will reach End of Life (EoL) in October 2025. **However, t\*\*\*\*his does not apply to Illumina instruments, see** [Windows 10 support and timelines for Illumina sequencing and array instrument computers](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000009668/?utm_source=agent\&utm_medium=email\&utm_campaign=kb) **for more information.** \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2247), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002247%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Reference Material Instrumentation > General > Reference Material * [AWS deprecation of TLS below v1.2 & impact to instruments connecting to Illumina BioInsight Platform](/instrumentation/general/instrumentation-general-reference_material-list/000008467) * [Antivirus recommendations for Illumina sequencing instruments](/instrumentation/general/instrumentation-general-reference_material-list/000002278) * [Approximate sizes of sequencing run output folders](/instrumentation/general/instrumentation-general-reference_material-list/000001508) * [Best Practices for Washes on the MiSeq](/instrumentation/general/instrumentation-general-reference_material-list/000001679) * [Best practices for getting the lab back up and running after an extended shutdown](/instrumentation/general/instrumentation-general-reference_material-list/000003153) * [Best practices for low diversity sequencing on the NextSeq 500/550 and MiniSeq systems](/instrumentation/general/instrumentation-general-reference_material-list/000002882) * [Best practices for maintaining and cleaning Illumina sequencing system wash cartridges](/instrumentation/general/instrumentation-general-reference_material-list/000005283) * [Best practices for maintaining the computer on Illumina sequencing systems](/instrumentation/general/instrumentation-general-reference_material-list/000005253) * [Bluekeep and DejaBlue two vulnerabilities of the Remote Desktop Protocol within Microsoft Windows](/instrumentation/general/instrumentation-general-reference_material-list/000001933) * [Calculating Percent Passing Filter for Patterned and Nonpatterned Flow Cells](/instrumentation/general/instrumentation-general-reference_material-list/000006309) * [Cluster density guidelines for Illumina sequencing platforms using non patterned flow cells](/instrumentation/general/instrumentation-general-reference_material-list/000001511) * [Configuring User Security Questions on the MiSeq i100 and NovaSeq X Series Platforms](/instrumentation/general/instrumentation-general-reference_material-list/000010191) * [Decontaminating Illumina instruments for novel coronavirus (2019 nCoV)](/instrumentation/general/instrumentation-general-reference_material-list/000002376) * [Diagnosing Suboptimal Clustering in Non patterned Flow Cells Video](/instrumentation/general/instrumentation-general-reference_material-list/000005788) * [Diagnosing Suboptimal Clustering in Patterned Flow Cells Video](/instrumentation/general/instrumentation-general-reference_material-list/000005789) * [Does my sequencing run look good?](/instrumentation/general/instrumentation-general-reference_material-list/000001922) * [End of Life (EOL) Sale and Support of the MiSeq RUO, MiniSeq and iSeq 100 Systems and Consumables](/instrumentation/general/instrumentation-general-reference_material-list/000009536) * [End to end sequencing and microarray training at Illumina Solutions Centers in the Americas](/instrumentation/general/instrumentation-general-reference_material-list/000008977) * [Features of Illumina Advantage (IA former TG) product](/instrumentation/general/instrumentation-general-reference_material-list/000005173) * [Focus images on the MiniSeq and NextSeq 500/550](/instrumentation/general/instrumentation-general-reference_material-list/000006325) * [Hard drives and computer information of the MiniSeq](/instrumentation/general/instrumentation-general-reference_material-list/000002013) * [Heat output specifications for Illumina sequencers](/instrumentation/general/instrumentation-general-reference_material-list/000008388) * [How Do I Prepare for My Illumina Instrument Delivery? Video](/instrumentation/general/instrumentation-general-reference_material-list/000005767) * [How To Power Cycle NovaSeq 6000 Video](/instrumentation/general/instrumentation-general-reference_material-list/000005611) * [How many cycles of SBS chemistry are in my kit?](/instrumentation/general/instrumentation-general-reference_material-list/000007002) * [How much PhiX spike in is recommended when sequencing low diversity libraries on Illumina platforms?](/instrumentation/general/instrumentation-general-reference_material-list/000001527) * [How to Clean Illumina Sequencer Wash Cartridges Video](/instrumentation/general/instrumentation-general-reference_material-list/000006608) * [How to Create a Sample Sheet in Local Run Manager](/instrumentation/general/instrumentation-general-reference_material-list/000008106) * [How to Disable Cloud Login Feature on the MiSeq i100 and NovaSeq X Series](/instrumentation/general/instrumentation-general-reference_material-list/000009462) * [How to Enable/Disable Illumina Proactive on the MiSeq](/instrumentation/general/instrumentation-general-reference_material-list/000002412) * [How to Enable/Disable Illumina Proactive on the NovaSeq 6000](/instrumentation/general/instrumentation-general-reference_material-list/000008507) * [How to Export Logs on the MiSeq i100 and NovaSeq X Series Instruments](/instrumentation/general/instrumentation-general-reference_material-list/000009265) * [How to Perform Washes on the MiSeq Video](/instrumentation/general/instrumentation-general-reference_material-list/000006958) * [How to Power Cycle the NextSeq 500/550](/instrumentation/general/instrumentation-general-reference_material-list/000001972) * [How to Power Cycle the NovaSeq 6000](/instrumentation/general/instrumentation-general-reference_material-list/000002470) * [How to Requeue an Analysis on BaseSpace Sequence Hub When No Changes to the Sample Sheet are Needed](/instrumentation/general/instrumentation-general-reference_material-list/000008380) * [How to achieve more consistent cluster density on Illumina sequencing platforms](/instrumentation/general/instrumentation-general-reference_material-list/000001481) * [How to add Illumina to TeamViewer allowlist](/instrumentation/general/instrumentation-general-reference_material-list/000003777) * [How to cache credentials for access to Network Storage and verify Read/Write access](/instrumentation/general/instrumentation-general-reference_material-list/000007828) * [How to change the Windows account type from administrator to standard](/instrumentation/general/instrumentation-general-reference_material-list/000007827) * [How to check .NET version on Windows instruments](/instrumentation/general/instrumentation-general-reference_material-list/000007801) * [How to check if a Windows account is a standard or administrator account](/instrumentation/general/instrumentation-general-reference_material-list/000007826) * [How to collect Group Policy Object (GPO) reports](/instrumentation/general/instrumentation-general-reference_material-list/000002273) * [How to connect benchtop instruments and Local Run Manager to a network location](/instrumentation/general/instrumentation-general-reference_material-list/000001934) * [How to disable and add exceptions to the Software Restriction Policies for TeamViewer in Windows 10](/instrumentation/general/instrumentation-general-reference_material-list/000006523) * [How to identify the IP and MAC address of a sequencing instrument](/instrumentation/general/instrumentation-general-reference_material-list/000002222) * [How to identify the UNC path of a network server or location.](/instrumentation/general/instrumentation-general-reference_material-list/000002274) * [How to import a pre existing index kits into Local Run Manager v3 and v4](/instrumentation/general/instrumentation-general-reference_material-list/000008929) * [How to install Windows critical security updates on Illumina instruments](/instrumentation/general/instrumentation-general-reference_material-list/000002282) * [How to interpret clusters passing filter in run metrics](/instrumentation/general/instrumentation-general-reference_material-list/000006529) * [How to invite users to a workgroup on BaseSpace Sequence Hub (Professional or Enterprise tier)](/instrumentation/general/instrumentation-general-reference_material-list/000002874) * [How to make sure Universal Copy Service is configured to Log On as a standard (non admin) account](/instrumentation/general/instrumentation-general-reference_material-list/000007852) * [How to recover passwords for Control Software accounts on the MiSeq i100 and NovaSeq X Series Instruments](/instrumentation/general/instrumentation-general-reference_material-list/000007773) * [How to requeue a NextSeq 1000/2000 run locally (on the instrument)](/instrumentation/general/instrumentation-general-reference_material-list/000005816) * [How to requeue and import run data for reanalysis with Local Run Manager](/instrumentation/general/instrumentation-general-reference_material-list/000001324) * [How to restart a sequencer after a power outage](/instrumentation/general/instrumentation-general-reference_material-list/000006975) * [How to set up a PhiX validation run with Local Run Manager](/instrumentation/general/instrumentation-general-reference_material-list/000001318) * [How to switch Operating System user accounts on Illumina Windows 10 Sequencing Systems](/instrumentation/general/instrumentation-general-reference_material-list/000007855) * [How to thaw and store sequencing reagents for optimal performance](/instrumentation/general/instrumentation-general-reference_material-list/000001533) * [How to update Network Credentials in Windows Credential Manager on Windows 10 Platforms](/instrumentation/general/instrumentation-general-reference_material-list/000010020) * [How to update Windows 10 account credentials on Benchtop Instruments](/instrumentation/general/instrumentation-general-reference_material-list/000001932) * [IT Requirements for Implementing Illumina Proactive Video](/instrumentation/general/instrumentation-general-reference_material-list/000005749) * [Illumina 测序平台的最大读长](/instrumentation/general/instrumentation-general-reference_material-list/000007102) * [Illumina测序平台上每个测序步骤的运行时间预测](/instrumentation/general/instrumentation-general-reference_material-list/000007137) * [Illumina测序平台测试Run中PhiX的上机浓度](/instrumentation/general/instrumentation-general-reference_material-list/000007139) * [Illumina测序系统废液中甲酰胺的终浓度是多少？](/instrumentation/general/instrumentation-general-reference_material-list/000007131) * [Illumina非Pattern Flow Cell测序平台簇密度推荐指南](/instrumentation/general/instrumentation-general-reference_material-list/000007415) * [Impact of ammonium based cleaning products on sequencing run performance](/instrumentation/general/instrumentation-general-reference_material-list/000001846) * [Index color balancing for XLEAP SBS reagents on the NextSeq 1000/2000 and NovaSeq X Series](/instrumentation/general/instrumentation-general-reference_material-list/000008422) * [Index color balancing for the NextSeq 500/550 and MiniSeq systems](/instrumentation/general/instrumentation-general-reference_material-list/000001241) * [Installing Reference Genomes on NovaSeq X Series Control Software v1.4](/instrumentation/general/instrumentation-general-reference_material-list/000010233) * [Instructions for thawing and storing NextSeq 500/550 reagents](/instrumentation/general/instrumentation-general-reference_material-list/000001974) * [Instrument Service Contract Plans](/instrumentation/general/instrumentation-general-reference_material-list/000003016) * [Instrument maintenance and shutdown procedures for extended site closures](/instrumentation/general/instrumentation-general-reference_material-list/000002336) * [Introducing TeamViewer for Remote Desktop Share with Illumina Support Teams](/instrumentation/general/instrumentation-general-reference_material-list/000003599) * [Introduction to Illumina Sequencing By Synthesis Support Webinar Video](/instrumentation/general/instrumentation-general-reference_material-list/000007983) * [Investigation of Log4j Vulnerability with Illumina instruments](/instrumentation/general/instrumentation-general-reference_material-list/000006291) * [Loading concentration considerations when migrating Illumina libraries between sequencing platforms](/instrumentation/general/instrumentation-general-reference_material-list/000001509) * [Maximum read length for Illumina sequencing platforms](/instrumentation/general/instrumentation-general-reference_material-list/000002826) * [Network Output Path Requirements in Local Run Manager and Universal Copy Service](/instrumentation/general/instrumentation-general-reference_material-list/000003683) * [NextSeq 500/550和MiniSeq测序系统上index混合的指导方针](/instrumentation/general/instrumentation-general-reference_material-list/000007297) * [NextSeq500/550和Miniseq平台进行低多样性文库测序的最佳操作](/instrumentation/general/instrumentation-general-reference_material-list/000007110) * [PhiX Indexed Control (1000 Cycle) Product Information](/instrumentation/general/instrumentation-general-reference_material-list/000009867) * [PhiX loading concentrations for validation runs on Illumina sequencing platforms](/instrumentation/general/instrumentation-general-reference_material-list/000001536) * [Plotting %Occupied by %PF to optimize loading for the NovaSeq X Series, NovaSeq 6000, MiSeq i100 Series, and iSeq 100](/instrumentation/general/instrumentation-general-reference_material-list/000002308) * [Plotting %Occupied by %Pass Filter to optimize loading for the NovaSeq 6000 and iSeq 100 Video](/instrumentation/general/instrumentation-general-reference_material-list/000005858) * [Quality Scores for Next Generation Sequencing](/instrumentation/general/instrumentation-general-reference_material-list/000006557) * [Reagent Stability and Thawing Guidelines for MiSeq Sequencing Kits](/instrumentation/general/instrumentation-general-reference_material-list/000001674) * [Run time estimates for each sequencing step on Illumina sequencing platforms](/instrumentation/general/instrumentation-general-reference_material-list/000001540) * [Security updates to address Windows Print Spooler Remote Code Execution Vulnerability](/instrumentation/general/instrumentation-general-reference_material-list/000007489) * [Sequencing Analysis Viewer (SAV) A Beginner's Guide Support Webinar Video](/instrumentation/general/instrumentation-general-reference_material-list/000007985) * [Sequencing Considerations for Low Diversity Samples Support Webinar Video](/instrumentation/general/instrumentation-general-reference_material-list/000007984) * [Serial number locations on Illumina sequencers](/instrumentation/general/instrumentation-general-reference_material-list/000006351) * [Sharing instrument performance data with Illumina Technical Support](/instrumentation/general/instrumentation-general-reference_material-list/000003400) * [Shelf life for Illumina reagent products](/instrumentation/general/instrumentation-general-reference_material-list/000003270) * [Troubleshooting "Cannot initiate communication with Universal Copy Service" error](/instrumentation/general/instrumentation-general-reference_material-list/000007067) * [Troubleshooting "Could not find a part of the path" errors on the NextSeq500/550 and MiniSeq](/instrumentation/general/instrumentation-general-reference_material-list/000009036) * [Uninterruptible Power Supply (UPS) Models by Instrument](/instrumentation/general/instrumentation-general-reference_material-list/000005838) * [Updating the Hostname or Domain Name on the MiSeq i100 Series](/instrumentation/general/instrumentation-general-reference_material-list/000009720) * [Using the MyIllumina dashboard to view instrument yield, Reads PF, and Q30 data as trends over time](/instrumentation/general/instrumentation-general-reference_material-list/000002125) * [Washes on the NovaSeq 6000](/instrumentation/general/instrumentation-general-reference_material-list/000002484) * [What is nucleotide diversity and why is it important?](/instrumentation/general/instrumentation-general-reference_material-list/000001543) * [What is the final formamide concentration in the waste solution of Illumina sequencing systems?](/instrumentation/general/instrumentation-general-reference_material-list/000001544) * [Why sequencing 26 or more cycles in Read 1 is recommended](/instrumentation/general/instrumentation-general-reference_material-list/000001891) * [Windows 10 support and timelines for Illumina sequencing and array instrument computers](/instrumentation/general/instrumentation-general-reference_material-list/000009668) * [为什么Read1测序读长推荐至少需要26个循环？](/instrumentation/general/instrumentation-general-reference_material-list/000007114) * [什么是核苷酸多样性，它为什么十分重要？](/instrumentation/general/instrumentation-general-reference_material-list/000007132) * [在Illumina平台进行低多样性文库测序时，应该掺入多少PhiX？](/instrumentation/general/instrumentation-general-reference_material-list/000007399) * [场地长期关闭或仪器长期不用时illumina仪器的维护与关机程序](/instrumentation/general/instrumentation-general-reference_material-list/000007310) * [如何在Illumina测序平台上获得更稳定的簇密度](/instrumentation/general/instrumentation-general-reference_material-list/000007398) * [如何更新UCS和LRM在Windows10系统中的凭据](/instrumentation/general/instrumentation-general-reference_material-list/000007099) * [我所购买的SBS试剂盒最多能够满足多少个循环的测序？](/instrumentation/general/instrumentation-general-reference_material-list/000007400) * [测序运行输出文件夹的近似大小](/instrumentation/general/instrumentation-general-reference_material-list/000007109) * [通过% Occupied和% Pass Filter散点图优化NovaSeq 6000和X、MiSeq i100和iSeq 100上样浓度](/instrumentation/general/instrumentation-general-reference_material-list/000007138) # AWS deprecation of TLS below v1.2 & impact to instruments connecting to Illumina BioInsight Platform **Background** Illumina BioInsight Platform Services, such as BaseSpace, Illumina BioInsight Platform Core (formerly, Illumina Connected Analytics (ICA)), and Proactive, run on Amazon Web Services (AWS). [AWS](https://aws.amazon.com/blogs/security/tls-1-2-required-for-aws-endpoints/) announced deprecation of TLS (Transport Layer Security) versions below 1.2 for all AWS service API endpoints. The encryption methods on many Illumina instruments currently use TLS v1.0 and TLS v1.1. To respond to evolving technology and conform to the most up to date security standards, AWS and other cloud providers will be updating the TLS configuration to a minimum version of TLS v1.2. While this change significantly improves Illumina security, it also means that beyond December 31st, 2023, certain instruments with control software versions indicated in Table 1, below, will not be able to connect or send data to the following. * BaseSpace Sequence Hub (BSSH) * Illumina BioInsight Platform Core * Checking and installing software updates online * Run monitoring through MyIllumina * Illumina Proactive Instrument users are urged to do **one of the following** below, listed in **order of priority**. **Option 1**: Upgrade to latest version of control software on instrument indicated in Table 1, below. **Option 2**: If upgrading is not an option, make sure that TLS 1.2 is enabled on the instrument using the instructions in the option 2 section, below. **Option 3:** If neither of the above actions can be taken, Illumina recommends setting up runs in local mode without connecting to any cloud services. ![](/files/2BAzJOX0hqwqDXNx2T61) ### **Note**: see detailed information for **Option 1**, **Option 2**, and **Option 3** below. ### **Option 1**: **Upgrade to latest control software version**. **Table 1**. Impacted instruments and mitigations for available instrument control software versions.
InstrumentImpacted Control SW versionsRequired upgraded versionField or user installable
MiSeqMiSeq Control Software (MCS) v4.0.x and earlierUpdate to MCS v4.1

Windows 7 upgrade requires field visit.

Windows 10 users can self-upgrade to MCS v4.1

NextSeq 500 /550NextSeq 500/550 Control Software (NCS) v4.0.x and earlierUpdate to NCS v4.2Requires field visit
NovaSeq 6000NovaSeq 6000 Control Software (NvCS) v1.7.5 and earlier *Update to NvCS v1.8.1User installable
MiniSeqMiniSeq Control Software (MnCS) v2.2 and earlier (all released versions)No new control software available
Use Option 2.		Not Applicable
iSeq 100 /NextSeq 1000/2000/ NovaSeq X Series/ iScan /Not impactedNot ApplicableNot Applicable
\*While NovaSeq 6000 control software versions 1.8.0 and 1.8.0.43 are not impacted, Illumina still recommends upgrading to latest control software version of 1.8.1. For any other instrument platforms, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support). ### ### **Option 2: Make sure that TLS v1.2 is enabled on the instrument.** TLS 1.2 Registry Patch instructions: **Note**: All steps must be run on a user account with administrator privileges. See the instructions to [check if running as administrator](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/How-to-check-if-a-Windows-account-is-a-standard-or-administrator-account-12/README.md) and how to [switch to an admin account](broken://pages/ykAxIQfMYRBuxekzFyMr). Start at step 1, below, for Windows 7 users only. For Windows 10, start at step 2. 1. Pre-requisite step for platforms that have Microsoft .NET Framework 4.5.1 or below. * Verify Microsoft .NET Framework version in Programs and Features. * If Microsoft .NET Framework is 4.5.1 or below, update to Microsoft .NET Framework 4.5.2 or above ([Microsoft hosted 4.5.2 offline installer](https://www.microsoft.com/en-us/download/details.aspx?id=42642)). * ![](/files/xrYrs98oblZjuqDblknP) * Power cycle the instrument 2. Close instrument control software. 3. Download [TLS1.2Registry.reg file from the Illumina support site](https://support.illumina.com/downloads/tls-1-2-registry-patch.html). 4. Move the TLS1.2Registry.reg file to C:\Illumina on instrument. * ![](/files/jEe3J9drT3CxDW8ooCtR) 5. Double click to run the file. Acknowledge pop-up message by selecting **Yes** to continue. * ![](/files/9jahXjPcsjHFQZEzPTB0) 6. Verify Success message by selecting **OK**. * ![](/files/HQFIBFV0Y9xEAUEkzsQ0) 7. Power cycle instrument and log back in as a standard (non-admin) account. ### **Option 3: Set up runs locally without connecting to any Illumina cloud services.** If neither Option 1 nor Option 2 can be performed, Illumina recommends setting up runs in local mode without connecting to any cloud services. Illumina also recommends turning off Proactive specifically for the [MiSeq](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/How-To-Enable-Illumina-Proactive-on-MiSeq/README.md) and [NovaSeq 6000](/instrumentation/general/instrumentation-general-reference_material-list/000008507) instruments to make sure that runs do not fail. Turning off Proactive will result in users losing the benefits of a [Proactive connection](https://www.illumina.com/services/instrument-services-training/product-support-services/instrument-monitoring.html) and this option should be used only as a last resort. ### **FAQs** **Is it okay if the TLS 1.2 Registry Patch was run twice?** Yes. The tool can be run multiple times without impact. **Do users need to re-validate after applying the registry patch?** Individual users must determine if they should re-validate. The registry update does not impact the sequencing software, analysis software, or resulting data and merely enables connection to BaseSpace and Proactive. **What should be done if the following error is seen?** ![](/files/qZSqY3XQ22GiFxIt53ms) Make sure TLS1.2Registry.reg file is in C:\Illumina, rerun TLS1.2Registry.reg, and verify success message by selecting **OK**. After verifying, power cycle the instrument. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8467), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008507%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Antivirus recommendations for Illumina sequencing instruments General antivirus (AV) and other Security information is available under the Antivirus Software and Configuration Guidelines section of the [Illumina Product Security Guidance](https://www.illumina.com/content/dam/illumina-support/documents/product-security/documentation-section/product-security-guidance/200055146_01_Illumina_Product_Security_Guidance.pdf). The whole of this document also details general instrument control computer best practices that should be considered in addition to recommendations for AV software configurations. To avoid data loss or interruptions, use the following guidelines to configure an antivirus software of your choice: * Configure software for manual scans and do not allow automatic scanning. * Perform manual scans only when the instrument is idle and not actively performing a sequencing run or analysis. * If possible, perform several sequencing runs with the AV software in listening or training mode to allow it to identify normal use patterns. * Set AV software updates to download without user authorization, but to not install automatically. * Install updates only when the instrument is not in use and the computer can be rebooted. * Do not allow the control computer to reboot automatically after install. * Exclude the application directory and data drives from any real-time file system protection. Apply this setting to the following drive locations: * C:\Illumina * C:\ProgramData\Illumina * D:\Illumina * Instrument specific folders:\ \- NextSeq 500/550 and MiniSeq: D:\Output\ \- NovaSeq 6000: Z:\outputfolder\ \- NextSeq1000/2000: /usr/local/illumina/images AND /usr/loca/illumina/runs\ \- NovaSeq X Series: /usr/local/illumina/runs AND /usr/local/illumina/mnt/runs\ \- **Note:** See the instrument **Site Prep Guide** for instrument specific details. * When deploying AV software across multiple instruments of the same model, install and configure the AV software on a subset of instruments first and monitor for any issues before expanding to additional instruments. For more details on configuring antivirus software for your system, see the **Site Prep Guide** for the instrument. Contact the antivirus software vendor for software-specific instructions. Reference： * [iSeq 100 Sequencing System Guide](https://support.illumina.com/downloads/iseq-100-system-guide.html) * [MiniSeq System Site Prep Guide](https://support.illumina.com/downloads/miniseq-site-prep-guide.html?langsel=/us/) * [MiSeq System Site Prep Guide](https://support.illumina.com/downloads/miseq_site_prep_guide_15027615.html?langsel=/us/) * [MiSeq i100 Series Product Documentation](https://support.illumina.com/sequencing/sequencing_instruments/miseq-i100-plus/documentation.html) * [NextSeq 500/550 Sequencing Systems Site Prep Guide](https://support.illumina.com/downloads/nextseq-site-prep-guide-15045113.html?langsel=/us/) * [NovaSeq 6000 Sequencing System Site Prep Guide](https://support.illumina.com/downloads/novaseq-site-prep-guide-1000000019360.html?langsel=/us/) * [NextSeq 1000/2000 Product Documentation](https://support.illumina.com/downloads/nextseq-1000-2000-product-documentation-200027171.html) * [NovaSeq X Series Product Documentation](https://support.illumina.com/downloads/novaseq-x-novaseq-x-plus-product-documentation.html) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2278), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002278%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Approximate sizes of sequencing run output folders **Background** The run folder sizes listed in this article are only an approximation based on dual-indexed runs with optimal cluster densities for each platform. For runs on nonpatterned flow cells, the size approximation is based on runs with clusters passing filter greater than 80%. The actual size will vary depending on the raw cluster density and the number of clusters passing filter for each run. Additional run folder size considerations: * iSeq 100, MiniSeq and NextSeq 500/550 (NextSeq Control Software v4.0 and higher) folder sizes include FASTQ files generated by the Local Run Manager FASTQ workflow. * MiSeq folder sizes include FASTQ files generated by either the MiSeq Reporter FASTQ workflow or the Local Run Manager FASTQ workflow (MiSeq Control Software 3.1 and higher). * NextSeq 1000/2000 folder sizes include local analysis output, which can add another 25-120+ GB depending on workflow. * NovaSeq 6000 folders do not include FASTQ files as part of the total output folder size as no onboard analysis is available for this platform. * The output folder size in the tables below is reported in Gigabytes (GB), except for the NovaSeq X which is reported in Terabytes (TB). Illumina recommends storing the output folder for iSeq 100, NextSeq 500/550, and NextSeq 1000/2000 runs on a network location. NovaSeq 6000 and NovaSeq X Series Control Software requires storing the output folder on a network location. **iSeq 100** | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 1.5 - 2.5 | **MiniSeq** Mid Output | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 2.3 - 2.6 | High Output | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 7.0 - 8.0 | | 2 x 75 | 6.0 - 8.0 | | 1 x 75 | 2.0 - 4.0 | Rapid | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 1 x 100 | 2 | **MiSeq** v3 chemistry | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 300 | 22 - 26 | | 2 x 75 | 19 - 22 | v2 chemistry | Read Length | Reagent Kit Configuration | Output Folder Size in GB | | ----------- | ------------------------- | ------------------------ | | 2 x 250 | Standard | 22 - 24 | | 2 x 250 | Nano | 1.6 - 1.8 | | 2 x 150 | Standard | 16 - 18 | | 2 x 150 | Micro | 3.0 - 5.0 | | 2 x 150 | Nano | 0.8 - 1.2 | | 2 x 25 | Standard | 14 - 16 | **MiSeq i100 Series** See Knowledge Article [Estimating Disk Space Utilization on the MiSeq i100 Series](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/MiSeq-i100-Disk-Estimation-Guide/README.md) **NextSeq 500/550** Mid Output | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 62 - 66 | | 2 x 75 | 39 - 46 | High Output | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 160 - 170 | | 2 x 75 | 92 - 97 | | 1 x 75 | 50 - 78 | **NextSeq 1000/2000 (Standard and XLEAP runs are expected to have similar sizes)** P1 | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 300 | 85-95 | | 2 x 150 | 50 - 55 | | 2 x 101 | 40 - 45 | | 2 x 75 | 35 - 40 | P2 | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 300 | 140-160 | | 2 x 150 | 89 - 99 | | 2 x 101 | 65 - 66 | | 2 x 75 | 44 - 55 | P3 | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 165 - 170 | | 2 x 101 | 103 - 126 | P4 (XLEAP Only) | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 170 - 180 | | 2 x 100 | 100 - 130 | | 2 x 50 | 70 - 80 | | 1 x 50 | 40 - 50 | **NovaSeq 6000** SP | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 1 x 36 | 20 | | 2 x 150 | 185 | | 2 x 250 | 400 | S1 | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 370 | S2 | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 2 x 150 | 730 | S4 | Read Length | Output Folder Size in GB | | ----------- | ------------------------ | | 1 x 36 | 240 | | 2 x 150 | 2190 | **NovaSeq X Series** Values listed below are PER FLOW cell in Terabytes (TB). 1.5B | Read Length | cBCL Only in TB | BCL Convert (GZIP) in TB | BCL Convert (ORA) in TB | | ----------- | --------------- | ------------------------ | ----------------------- | | 2 x 50 | 0.054 - 0.091 | 0.132 - 0.221 | 0.086 - 0.143 | | 2 x 100 | 0.106 - 0.181 | 0.265 - 0.442 | 0.173 - 0.286 | | 2 x 150 | 0.163 - 0.272 | 0.397- 0.662 | 0.259 - 0.429 | 10B | Read Length | cBCL Only in TB | BCL Convert (GZIP) in TB | BCL Convert (ORA) in TB | | ----------- | --------------- | ------------------------ | ----------------------- | | 2 x 50 | 0.34 - 0.57 | 0.83 - 1.38 | 0.54 - 0.89 | | 2 x 100 | 0.68 - 1.13 | 1.65 - 2.76 | 1.08 - 1.79 | | 2 x 150 | 1.02 - 1.70 | 2.48 - 4.14 | 1.62 - 2.68 | 25B | Read Length | cBCL Only in TB | BCL Convert (GZIP) in TB | BCL Convert (ORA) in TB | | ----------- | --------------- | ------------------------ | ----------------------- | | 2 x 50 | 0.85 - 1.42 | 2.07 - 3.45 | 1.35 - 2.23 | | 2 x 100 | 1.70 - 2.83 | 4.13 - 6.90 | 2.70 - 4.47 | | 2 x 150 | 2.55 - 4.25 | 6.200 - 10.35 | 4.05 - 6.70 | DRAGEN Analysis files can ADD the following additional data in terabytes (TB) to the expected Output folder size based on Analysis options selected. Approximate file sizes are based on a single flow cell, 2x150 cycle sequencing run. | Flow Cell Type | BAM (TB) | CRAM (TB) | GVCF+VCF (TB) | | -------------- | -------- | --------- | ------------- | | 1.5B | 0.4 | 0.1 | <0.1 | | 10B | 2.5 | 1.0 | 0.2 | | 25B | 6.3 | 2.5 | 0.5 | \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1508), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009356%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Best Practices for Washes on the MiSeq **Background** Many factors contribute to a successful sequencing run. One important maintenance practice is to ensure the system's fluidic lines are thoroughly washed between sequencing runs. It is also important that the fluidics systems are well maintained when the instrument is idle. This ensures that traces of old reagents are washed out so they cannot negatively impact sequencing performance. This article outlines all different types of washes on the MiSeq and when they should be performed. **Note:** When any wash is complete, leave the used flow cell, wash tray, and wash bottle containing the remaining wash solution in the instrument. The sippers remain in the down position, preventing the sippers from drying out and air from entering the system. **Best Practices for Wash Solution** Always make fresh wash solution for each wash. Use fresh Tween-20 and molecular-biology grade water. Older, dilute solutions of Tween-20 can encourage microbial growth and be detrimental to system performance. **Wash Times** * Post-Run wash: 20 minutes. * Post-Run wash with Template line wash: 30 minutes. * Maintenance wash: 90 minutes. * Standby wash: 2 hours. **Post-Run Wash:** * Required after every sequencing run. At end of complete run, the MiSeq Control Software (MCS) will guide to set up the post-run wash. * One step wash with 0.5% Tween 20 wash solution. * 1. Add 6 ml wash solution to each reservoir of the wash tray. 2. Add 350 ml wash solution to the 500 ml wash bottle. 3. If the run showed no performance issues, you can use the old experimental flow cell to conduct the wash * Expected wash waste volumes: 17.25 mls. **Template Line Wash:** * **Optional** for Research Use Only (RUO) runs. Can reduce trace sample carry-over contamination. * Additional step to the regular post-run wash, with 0.5% Tween 20 wash solution. * 1. Add 6 ml wash solution to each reservoir of the wash tray. 2. Add 350 ml wash solution to the 500 ml wash bottle. 3. Add 0.01% sodium hypochlorite (NaOCl, lab grade bleach) to the disposable wash tube in position 17 of the wash tray.\ \* **NOTE**: It is important to make fresh NaOCl dilutions from stock. * Expected wash waste volumes: 25.50 mls. **Maintenance Wash**: * Required every 30 days. * The instrument will display a warning notification that a maintenance wash is required 30 days from the last maintenance wash. * The instrument will prevent the user from starting a new sequencing run if a maintenance wash has not been completed within the previous 45 days. * Involves **three** wash steps with 0.5% Tween 20 wash solution (prepared fresh for each wash step). MCS will guide on when to empty waste and refill the wash solutions for all three washes. 1. Add 6 ml wash solution to each reservoir of the wash tray. 2. Add 350 ml wash solution to the 500 ml wash bottle. * Expected wash waste volumes: 51.75 ml. **Standby Wash:** * Prepares instrument for Standby mode. * Perform a standby wash if the instrument is unused for > 7 days and every 30 days thereafter if the instrument remains idle. * Includes **two** wash steps with 0.5% Tween 20 wash solution (prepared fresh for each wash step). MCS will guide on when to empty waste and refill the wash solutions for both washes. 1. Add 6 ml wash solution to each reservoir of the wash tray. 2. Add 350 ml wash solution to the 500 ml wash bottle. * When the Standby wash is complete, the instrument will be in **Standby** mode and a message appears on the home screen indicating the status of the instrument. * To return the instrument to **Sequencing** mode, [power cycle](https://knowledge.illumina.com/instrumentation/miseq/instrumentation-miseq-reference_material-list/000001894) the instrument to reset system communications, then conduct a **Maintainance Wash** to bring the instrument out of standby mode. * Expected wash waste volumes: 46.0 mls. Additional information, please reference [MiSeq System Product Documentation](https://sapac.support.illumina.com/sequencing/sequencing_instruments/miseq/documentation.html). \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1679), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001679%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Best practices for getting the lab back up and running after an extended shutdown When returning to the lab after an extended shutdown or inactivity, it is important to make sure all lab resources are up and running and ready to be used. Below are best practices to check library prep, sequencing and microarray reagents and instruments to ensure a successful reopening. **Laboratory and Reagent Checks** Wipe down all lab surfaces with 10% bleach to remove any accumulated dust or contaminants. * Pay particular attention to typical ‘hot spots’: * Benchtops used for processing amplified DNA * Door handles * Refrigerator and freezer door handles * Computer keyboard and mouse * Centrifuges, vortexers, and thermal cyclers * Clean all equipment in any pre-amp areas (including pipettes) * Refer to the article [Impact of ammonium-based cleaning products on sequencing run performance](/instrumentation/general/instrumentation-general-reference_material-list/000001846) for additional details Proper storage and handling of reagents, kits, and user-supplied materials should be followed according to documented procedures. Check connectivity to network drives or servers used for file storage (output run folders, manifest files, cluster files, DMAPs) or data processing (IDAT repository). **Sequencing Instrumentation Considerations** Instrument System Guides:\ [iSeq 100](https://support.illumina.com/downloads/iseq-100-system-guide.html) | [MiniSeq](https://support.illumina.com/downloads/miniseq-system-guide-1000000002695.html) | [MiSeq](https://support.illumina.com/sequencing/sequencing_instruments/miseq/documentation.html) | [MiSeq i100](https://support.illumina.com/sequencing/sequencing_instruments/miseq-i100-plus.html) | [NextSeq 500/550](https://support.illumina.com/downloads/nextseq-500-550-systems-product-documentation.html) | [NextSeq 1000/2000](https://support.illumina.com/downloads/nextseq-1000-2000-product-documentation-200027171.html) | [NovaSeq 6000](https://support.illumina.com/downloads/novaseq-6000-system-guide-1000000019358.html) | [NovaSeq X Plus](https://support.illumina.com/downloads/novaseq-x-novaseq-x-plus-product-documentation.html) For instruments that were left on: 1. Confirm the recommended maintenance/manual/standby washes were performed per the appropriate system guide. 2. Perform a full power cycle, following the steps in the system guide. 3. Leave system off for at least 5 minutes before powering back on. **Note:** While the iSeq 100, NextSeq 1000/2000, and MiSeq i100do not have onboard fluidics, a power cycle is recommended for these instruments as well. For instruments that were turned off: 1. Power on the instrument and verify the control software initializes. 2. Perform two maintenance/manual washes to rehydrate the fluidics system (excluding iSeq 100, NextSeq 1000/2000 and MiSeq i100). **Note:** If an additional maintenance/manual/standby wash using laboratory-grade water was not performed prior to instrument shutdown, perform three maintenance/manual washes to rehydrate the fluidics system, then run System Checks to test the fluidics delivery. System Check details are found in the appropriate system guides. **Library Preparation Considerations** Starting a New Library Prep * When starting new library preparation, Illumina recommends reviewing the best practices for the specific library prep kit being used. This information is found on the appropriate product support page. Proceeding to a Sequencing Run with Stored Libraries * For any Illumina library that has been stored for longer than the recommended time, as specified in the reference guide, Illumina recommends repeating quality control (QC) and quantification prior to sequencing. Re-QC is beneficial because libraries can degrade during prolonged storage, leading to loss of overall yield. Recommended QC methods for most Illumina libraries are summarized in the [Library quantification and quality control quick reference guide](/library-preparation/general-library-prep/library-preparation-general-library-prep-reference_material-list/000001247) support bulletin. For libraries requiring bead-based normalization, Illumina recommends storing the library at the last safe stopping point, just prior to the bead-based normalization step, as specified in the protocol guide. Libraries stored as double stranded DNA (dsDNA, before bead-based normalization) are more stable than libraries stored as single stranded DNA (ssDNA, after bead-based normalization). If a library has been stored long term after bead-based normalization, Illumina recommends repeating the bead-based normalization of the original dsDNA library. **Infinium Assay Considerations** * Refer to [Infinium Assay Lab Setup and Best Practices](https://support.illumina.com/downloads/infinium-assay-lab-setup-and-procedures-11322460.html) and the appropriate Infinium Assay Reference Guide to make sure that all equipment and hardware are present and in good working condition. * Note the duration and temperature recommendations for MSA plate storage stated in the ‘Safe Stopping Point’ portions of the [Infinium Assay Reference Guide](https://support.illumina.com/downloads/infinium-hts-assay-reference-guide-15045738.html). * Check stocks of user-supplied materials (eg, cap mats, 96-well plates, gloves, etc.) that may have been consumed by other groups using the space in the interim. * Thoroughly wash glass back plates that may have accumulated dust or residue during the time of disuse. See the articles [Best practices for glass back plate care and handling for Infinium HD, HTS, LCG, and XT assays](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Microarray-Best-Practices-for-Glass-Back-Plate-Care-and-Handling/README.md) and [XStain glass back plate care recommendations for Infinium EX Assays](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/XStain-glass-back-plate-care-recommendations-for-Infinium-EX-Assays/README.md) for details. Te-Flow and Water Circulator: 1. Confirm that there is no microbial growth in the water circulator and that the water is at the proper fill level. 1. If microbial growth is present, see the following instructions for cleaning the water circulator and refresh with algicide if needed: [Care and Preventive Maintenance for Water Baths and Chillers](https://www.coleparmer.com/tech-article/water-bath-chiller-care-maintenance). 2. Do not use chlorine bleach to clean the water circulator. 2. Check the waste tubing lines of the Te-Flow and white reagent pan. Bleach can be squirted through the waste tubing lines leading to the waste carboy to clean them, if needed. 3. If the waste carboy has been emptied or moved, make sure it is returned to its proper position, with an unimpeded, gravity-driven flow of waste from the Te-Flow Reagent pan to the waste carboy. Make sure that waste tubing is not kinked and there are no ‘uphill’ runs to the waste carboy. Tecan/Illumina Automated Pipetting System (IAPS): 1. If the Tecan fluidics were stored dry, refill the system water carboy. 2. Empty the waste liquid container and disposable tip waste bag, if necessary. 3. Make sure that the Te-Flow is seated correctly in the pan, and that the Te-Flow is in the appropriate location on the Tecan deck. 4. Power on the Tecan. 5. Refer to the following sections in the [Infinium Assay Lab Setup and Procedures Guide](https://support.illumina.com/downloads/infinium-assay-lab-setup-and-procedures-11322460.html) under Robot Usage and Maintenance: 1. **Preparing the Infinium Automated Pipetting System for Use** (perform at least two bleach washes) * **Note**: if the system was idle for a long time and/or dried out prior to shut down, multiple System Wash cycles are needed to purge all air from the fluidics. 2. **Testing Volume Accuracy of the IAPS Tips** iScan 1. Power on the scanner and make sure that the Archimedes drive appears on the PC before launching iScan Control Software (ICS). 2. Clean the BeadChip carriers and iScan Nest (tray that carrier is placed on) with an Ethanol wipe to remove any dust or built up residue. 3. Turn on the scanner at least 30 minutes before use to allow the lasers to warm up. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #3153), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008440%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Best practices for low diversity sequencing on the NextSeq 500/550 and MiniSeq systems Accurate and robust sequencing of [low diversity or unbalanced composition libraries](/instrumentation/general/instrumentation-general-reference_material-list/000001543) on the NextSeq 500/550 and MiniSeq requires well-designed experiments and informatics pipelines. A common example of a low diversity library is an amplicon-based library preparation method, such as 16S metagenomics. These libraries tend to have DNA sequences that start at the same location (ie, the probe binding site) and are mostly identical. A single represented locus causes a biased base composition that can change drastically from cycle to cycle. The NextSeq 500/550 and MiniSeq systems use [2-channel sequencing chemistry](https://www.illumina.com/science/technology/next-generation-sequencing/sequencing-technology/2-channel-sbs.html). Therefore, it is important to have all four DNA bases represented in every cycle, in order for the software to correctly identify DNA clusters and perform accurate base calling. To meet this requirement using a low diversity library, Illumina recommends experimental designs that provide cycle-to-cycle diversity using the following methods: * Use indexing to add multiple, indexed samples from various applications to the run. * Indexed samples from applications that are more diverse, such as human amplicon sequencing, enrichment, or whole-genome sequencing, can be used to balance diversity. * For best results, sequence multiple samples on the same flow cell using single- or dual-indexing. * Spike-in [PhiX control V3 Library](/library-preparation/general-library-prep/library-preparation-general-library-prep-reference_material-list/000001545) to the run. * A good starting point is to use 50% [PhiX](https://www.illumina.com/products/by-type/sequencing-kits/cluster-gen-sequencing-reagents/phix-control-v3.html) and then titrate the amount down, based on the quality of the primary and secondary analysis results. The presence of the spiked-in sample provides the necessary cycle-to-cycle base diversity. * Aim to [target a cluster density 30-40%](/instrumentation/general/instrumentation-general-reference_material-list/000001527) beneath the recommended cluster density range for balanced libraries (such as PhiX) on NextSeq and MiniSeq systems. * MiniSeq reagents accommodate an optimal raw cluster density of 170-220 K/mm2 for balanced libraries * NextSeq 500/550 reagents accommodate an optimal raw cluster density of 170-220 K/mm2 for balanced libraries The design recommendations in this article enable the NextSeq 500/550 and MiniSeq systems to sequence low diversity libraries. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2882), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001527%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Best practices for maintaining and cleaning Illumina sequencing system wash cartridges Illumina sequencing platforms with on board fluidics systems require a post-run wash and/or maintenance wash to be performed with regularity (refer to the appropriate instrument guide for details). To avoid contaminating the fluidics lines during these washes, Illumina recommends following these best practices. 1. After removing the wash cartridge from the instrument, properly discard any remaining wash solution (eg, do not reuse the Tween wash solution). 2. Thoroughly rinse each position of the wash cartridge with lab-grade warm water. 3. Place the wash cartridge upside down with sufficient clearance to allow airflow and proper drying. 4. Inspect the wash cartridge wells regularly for contamination (refer to Figure. 1, black or pink discoloration may be noted). ![](/files/Vg8kBcKWNtcuLucRoxmU) **Figure 1**. Black ring at bottom of wash cartridge well. If there is contamination in the well, please clean the wash cartridge as follows: 1. Prepare a 1-3% lab-grade bleach solution to fill the wells of the tray. 2. Use a brush to remove the mold from the wells. 3. **IMPORTANT:** Thoroughly rinse the wells (at least three times) with DI or lab-grade water (residual bleach can cause clustering issues on subsequent runs). 4. Place cartridge upside down with sufficient clearance to allow airflow and proper drying. 5. Repeat as necessary if mold is still present. 6. If it is not possible to remove all the mold, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) to discuss wash cartridge replacement. For step-by-step guidance, refer to this. **Resources** * [MiniSeq System Guide](https://support.illumina.com/sequencing/sequencing_instruments/miniseq/documentation.html) * [MiSeq System Guide](https://support.illumina.com/sequencing/sequencing_instruments/miseq/documentation.html) * [NextSeq 550 System Guide](https://support.illumina.com/sequencing/sequencing_instruments/nextseq-550/documentation.html) * [NovaSeq 6000 Sequencing System Guide](https://support.illumina.com/sequencing/sequencing_instruments/novaseq-6000/documentation.html) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5283), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005283%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Best practices for maintaining the computer on Illumina sequencing systems Proper maintenance of the instrument computer minimizes computer-related issues during sequencing runs. The following tips help maintain the instrument computer. How often these maintenance steps are recommended is dependent on the usage of the instrument. **Power cycle the computer and instrument** Power cycling resets the instrument computer, memory usage, and software programs. A power cycle consists of shutting down the instrument and computer, leaving the system off for two to five minutes, then restarting the instrument and computer. The instrument [System Guides](https://support.illumina.com/documentation.html) contain recommendations for properly power cycling. * Instruments should be left on at all times when not being power cycled to maintain the integrity of the instrument fluidics. * Power cycling the instrument computer regularly can maintain consistent instrument computer performance. * Power cycling the instrument may be required during troubleshooting. * The instrument system guides contain recommendations for properly shutting down the instrument and computer for extended periods of time. **Cleaning the hard drives** **iSeq 100** Temporary run folders, or “temp folders”, are not deleted by default on the iSeq 100. Without removal, old run folders will reduce hard drive space. The temp folders (D:\Illumina\iSeq Runs) can be managed by deleting the run via Process Management in the control software. Runs in the default output folder on the instrument (D:\SequencingRuns) can only be deleted via the file explorer. **MiniSeq** Temp run folders are not deleted by default on the MiniSeq. Without removal, old run folders will reduce hard drive space. Local Run Manager can be configured for automated deletion of analysis folders, and folder retention time is configured in the Local Run Manager System Settings. Otherwise, run folders require manual deletion. **MiSeq** The hard drive on the MiSeq is configured for processing runs and performing on-instrument analyses and is not meant for long-term storage. Data within the MiSeqTemp folder is automatically cleared after 7 days. It is a good practice to move old run folders from the MiSeqAnalysis and MiSeqOutput folders to long-term storage regularly. **MiSeq i100 Series** The MiSeq i100 Series instruments run in Kiosk Mode to prevent unauthorized users from accessing the operating system. MiSeq i100 Series run folders are not automatically deleted. If there is insufficient data storage space, a warning notification displays during pre-run checks. Regularly deleting run folders is recommended. See [Run Management](https://support-docs.illumina.com/IN/MiSeqi100Series/Content/IN/MiSeqi100/RunMgmt.htm?Highlight=delete%20run) for instructions to delete runs. **NextSeq 500/550** * **With NextSeq Control Software v2**The NextSeq hard drive is designed to store data for one run, which will be automatically overwritten when a new run is started. * **With NextSeq Control Software v4**The NextSeq hard drive can store multiple runs, but it is recommended to use an output folder in a network location. The data in the temp folder is automatically overwritten when a new run is started. Output folders on the instrument require manual deletion. **NovaSeq 6000** NovaSeq 6000 temp run folders are not automatically deleted. Without removal, hard drive space can become limited, which can impact data processing. Regularly deleting run folders is recommended. Delete runs from the temp folders via Process Management in the control software. **NextSeq 1000/2000** NextSeq 1000/2000 run folders are not automatically deleted. Without removal, hard drive space can become limited, which can impact data processing. Regularly deleting run folders is recommended. Delete runs from the temp folders via Disk Management in the control software. Deleting runs manually via the file navigation system can negatively impact the control software. **NovaSeq X Series** NovaSeq X Series run folders are not automatically deleted. If there is insufficient data storage space, a warning notification displays during pre-run checks. Regularly deleting run folders is recommended. See [Clear Hard Drive Space](https://support-docs.illumina.com/IN/NovaSeqX/Content/IN/NovaSeqX/ClearSpace.htm) for instructions to delete runs. Deleting runs manually via the file navigation system can negatively impact the control software. **Security best practice** The [Illumina Security and Networking](https://support.illumina.com/product-security-portal.html) web page contains recommendations for security configurations on all Illumina sequencing platforms. Further platform-specific recommendations are found in the instrument site prep guides. It is important that installed antivirus software does not interfere with sequencing runs. For more information, refer to the site prep guide for your system. * [iSeq 100 Sequencing System Guide](https://support.illumina.com/downloads/iseq-100-system-guide.html) * [MiniSeq System Site Prep Guide](https://support.illumina.com/downloads/miniseq-site-prep-guide.html?langsel=/us/) * [MiSeq System Site Prep Guide](https://support.illumina.com/downloads/miseq_site_prep_guide_15027615.html?langsel=/us/) * [MiSeq i100 Series Product Documentation](https://support.illumina.com/sequencing/sequencing_instruments/miseq-i100-plus/documentation.html) * [NextSeq 500/550 Sequencing Systems Site Prep Guide](https://support.illumina.com/downloads/nextseq-site-prep-guide-15045113.html?langsel=/us/) * [NovaSeq 6000 Sequencing System Site Prep Guide](https://support.illumina.com/downloads/novaseq-site-prep-guide-1000000019360.html?langsel=/us/) * [NextSeq 1000/2000 Product Documentation](https://support.illumina.com/downloads/nextseq-1000-2000-product-documentation-200027171.html) * [NovaSeq X Series Product Documentation](https://support.illumina.com/downloads/novaseq-x-novaseq-x-plus-product-documentation.html) **Language and Regional settings** Instrument computer language and regional settings are set to English (United States) by default. Do not change this setting. The software is not designed to run in another language. Changing this setting can cause secondary analysis failures and communication problems between the computer and the instrument. Daylight saving settings are enabled by default for correct syncing with BaseSpace Sequence Hub. Do not change this setting. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5253), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005253%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Bluekeep and DejaBlue two vulnerabilities of the Remote Desktop Protocol within Microsoft Windows Recently, several vulnerabilities around the Remote Desktop Protocol (RDP) within Microsoft Windows systems were disclosed (Bluekeep and DejaBlue). While these vulnerabilities apply to all Illumina systems, there have been no reported infections of Illumina systems. **How to Secure Your Systems** * As recommended in the [Illumina Security Best Practices Guide](https://www.illumina.com/content/dam/illumina-support/documents/product-security/documentation-section/product-security-guidance/200055146_01_Illumina_Product_Security_Guidance.pdf), RDP should be disabled on all Illumina instruments. * More details about the BlueKeep vulnerability can be found [here](https://www.microsoft.com/en-us/security/blog/2019/08/08/protect-against-bluekeep/). **Note: the BlueKeep RDP patch applies to only instruments running on Windows 7, while DejaBlue RDP patch applies to all instruments and Windows operating systems.** For DejaBlue, Illumina recommends the application of the specific patch for your instrument. Use the table below to select the appropriate patches. Due to prerequisites, the patches should be installed in numerical order (eg, Patch 1 first, Patch 2 second, Patch 3 (as applicable) last). | Operating System | PATCH 1 | PATCH 2 | PATCH 3 | | ---------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Windows 10 |

Patch1

2019-09 Servicing Stack Update for Windows 10 Version 1607 for x86-based Systems (KB4512574)

|

Patch 2

2019-07 Cumulative Update for Windows 10 Version 1607 for x64-based Systems (KB4512517)

| N/A | | Windows 7 |

Patch1

2019-09 Security Update for Windows Embedded Standard 7 for x64-based Systems (KB4474419)

|

Patch2

2019-03 Servicing Stack Update for Windows Embedded Standard 7 for x64-based Systems (KB4490628)

|

Patch3

2019-08 Security Only Quality Update for Windows Embedded Standard 7 for x64-based Systems (KB4512486)

| The security of your data and systems is paramount to Illumina. If you have additional questions regarding security recommendations from Illumina or about RDP on your Illumina systems, refer to the [Product Security Portal](https://support.illumina.com/product-security-portal.html) page on the Illumina website or contact . \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1933), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001933%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Calculating Percent Passing Filter for Patterned and Nonpatterned Flow Cells **Introduction**The latest innovation in flow cell technology is the development of the patterned flow cell. Five Illumina sequencing platforms currently take advantage of this advanced technology: the iSeq 100, MiSeq i100 Series, NextSeq 1000/2000, NovaSeq 6000 and NovaSeq X Series System. Patterned flow cells consist of a nano well substrate with billions of ordered wells (Figure 1A). Compared to nonpatterned flow cells (Figure 1B), the uniform cluster sizes enable optimal spacing and increased cluster density. Although the ordered spacing of patterned flow cells enables significantly higher cluster density, patterned flow cells also report comparatively lower percent passing filter (%PF) values\* due to differences in the %PF calculation method. This technical note outlines these differences and describes how they lead to lower %PF metrics for patterned flow cells. **Percent Passing Filter with Nonpatterned Flow Cells** Real-Time Analysis (RTA) software proceeds through several stages including image analysis, template generation, base calling, passing filter calculations, and quality scoring. Template generation occurs during cycles 1-5 of Read 1 and defines the position of each cluster in a tile. The template is used as a reference for registration and intensity extraction during subsequent sequencing cycles. With nonpatterned flow cells, dim or low-quality clusters are removed from the raw cluster count during template generation (Figure 2). This effectively acts as a prefiltration step, removing clusters unlikely to pass filter in the first 25 sequencing cycles and yielding relatively high %PF values. **Percent Passing Filter with Patterned Flow Cells** With patterned flow cells, the calculation of %PF is different because there is no template generation step—fixed cluster locations eliminate the need for template generation. Because template generation and the associated preliminary filtration steps are not applied, empty wells or clusters that may be dim, low quality, or polyclonal are included in the raw cluster count, which leads to lower %PF values. Although the percent passing filter metric will be much lower with patterned flow cells, it will not impact performance or data quality. **Summary** Due to the differences in the %PF calculation methods, patterned flow cells have artificially lower %PF metrics compared to nonpatterned flow cells. With patterned flow cells, there is no template generation or preliminary filtration step during image analysis, which results in lower %PF values. Although the %PF values are lower, the uniform feature sizes and optimal spacing enable significantly increased cluster density for patterned flow cells. **\*** The %PF calculations involve the application of a chastity filter to each cluster. Chastity is defined as the ratio of the brightest base intensity divided by the sum of the brightest and second brightest base intensities. Clusters “pass filter” if no more than 1 base call has a chastity value below 0.6 in the first 25 cycles. This filtration process removes the least reliable clusters from the image analysis results. ![](/files/xfGag5ioeY7xgxLOMjhK) ![Figure 2. Patterned Flow Cells and %PF..PNG](/files/KT95dqscgdj5M1E0RPlF) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6309), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006309%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Cluster density guidelines for Illumina sequencing platforms using non patterned flow cells Cluster density is an important factor in optimizing data quality and yield. The following table lists the recommended raw cluster densities for balanced libraries (such as PhiX): ![](/files/2MauXldgPEYqW66THnxp) The iSeq 100, MiSeq i100 Series, NextSeq 1000/2000, NovaSeq 6000, and NovaSeq X Series systems utilize patterned flow cells. This results in a fixed cluster density, even if all nanowells are not occupied. In these systems, monitoring the Cluster Pass filter (%) is a better measure of potential cluster occupancy. See the following for further details: * [Plotting %Occupied by %PF to optimize loading for the NovaSeq 6000 and X, MiSeq i100, and iSeq 100](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Plotting-Occupied-by-Pass-Filter-to-optimize-loading-concentration-for-NovaSeq-and-iSeq-100-platforms-support-bulletin/README.md) * [Calculating Percent Passing Filter for Patterned and Nonpatterned Flow Cells](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Calculating-Percent-Passing-Filter-for-Patterned-and-Nonpatterned-Flow-Cell/README.md) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1511), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006309%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Configuring User Security Questions on the MiSeq i100 and NovaSeq X Series Platforms **Background** Control Software User accounts have the option to configure Security Questions that can be used for Password Recovery. See the following steps to configure the Security Questions for specific User accounts on the MiSeq i100 and NovaSeq X Series instruments. **Configure remote Illumina Run Manager access (MiSeq i100 Series only)** The Security Questions can only be configured through the Illumina Run Manager user interface (UI), which is only accessible through remote access for the MiSeq i100 Series. See Knowledge Article [How to Setup a Remote Connection to Illumina Run Manager on the MiSeq i100 Series Instruments](/instrumentation/miseq-i100-series/instrumentation-miseq-i100-series-reference_material-list/000009334) for configuration details before proceeding with configuring Security Questions. **Configuring Security Questions** 1. Access the Illumina Run Manager UI: 1. NovaSeq X Series: 1. **Minimize** the NovaSeq X Series Control Software. 2. In the Linux Operating System (OS), select **Activities** and then open **Chromium**. 3. In the address bar, type in `localhost` and press **Enter**. 4. If prompted about an unsafe connection, select **Advanced** and then **Proceed (unsafe)...** 2. MiSeq i100 Series: 1. From a remote computer on the **same** network, open a support Internet browser. 2. In the address bar, type in the instrument `hostname` or `fully-qualified domain name` and press **Enter**. 2. Login to the Illumina Run Manager UI with the **User account** that will configure their Security Questions. 3. Select the **User icon** in the top-right corner, then select **Edit Security Questions** (Figure 1). 4. For each **Security Question**, select the question using the **dropdown menu** and then type in the appropriate answer (Figure 2), then select **Save**. 5. Select the **User icon** in the top-right corner, then select **Sign out** (Figure 1). ![](/files/Co3ZUtZLmBYKcNF6wh9w) **Figure 1**: The User menu showing Edit Security Questions and Sign out options. ![](/files/KaOeO72cWe34K3MA9UFl) **Figure 2:** Menu showing examples of security questions and corresponding answers. \ \ \
| | | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #10191), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009334%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Decontaminating Illumina instruments for novel coronavirus (2019 nCoV) See [Illumina Statement on Novel Coronavirus](https://www.illumina.com/company/news-center/feature-articles/illumina-statement-on-novel-coronavirus.html) and follow the [Illumina Perspective on the Novel Coronavirus SARS-CoV-2 (2019-nCoV) Outbreak](https://www.illumina.com/company/news-center/feature-articles/illumina-perspective-on-the-novel-coronavirus--covid-19--outbrea.html) web page for further updates. **General Guidelines for Decontaminating Illumina Systems** In keeping with recommendations from the United States CDC and World Health Organization (WHO), Illumina recommends the following procedure for decontaminating instruments suspected or known to have come in contact with novel coronavirus (2019-nCoV): **Decontamination steps** 1. Wear appropriate personal protective equipment before entering a contaminated space 2. Perform a maintenance wash with laboratory-grade water to flush the fluidics systems 3. Shut down the instrument and unplug the instrument from power outlets prior to applying any cleaning agent 1. Refer to the specific instrument system guide for appropriate shutdown procedures 4. Spray all accessible components and surfaces with a 10% bleach solution and allow solution to remain on the surface for at least 10 minutes 1. Select the appropriate spray pattern to avoid splashing of the bleach solution 2. Use a pre saturated wipe for sensitive electronic equipment 3. Use a pre saturated wipe to decontaminate the touchscreen, mouse, or keyboard 5. After the minimum 10 minute contact time, use a heavy-duty wipe to remove excess bleach before it dries\ **IMPORTANT:** Any exposed parts consisting of stainless steel or aluminum should then be wiped down with a 70% ethanol solution to remove excess bleach 1. The 70% ethanol solution should be wiped off with a heavy-duty wipe before it dries 2. Use caution when using ethanol near ignition sources such as electrical outlets 6. Make sure that all the following accessible components and surfaces are cleaned: 1. Outer skins of the instrument 2. Doors and parts accessible to the user 3. Rear of instrument, accessible tubes, and cords 4. Particular emphasis should be placed on: * Areas where samples are loaded and processed * Peripherals that are contacted during normal instrument use such as touch screens, mouse devices, and keyboards **Additional Resources** World Health Organization (WHO) Guidance * [Laboratory biosafety guidance related to the novel coronavirus](https://www.who.int/docs/default-source/coronaviruse/laboratory-biosafety-novel-coronavirus-version-1-1.pdf?sfvrsn=912a9847_2) Illumina Support Bulletins: * [Impact of ammonium-based cleaning products on sequencing run performance](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000001846) * [Instrument maintenance and shutdown procedures for extended site closures](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000002336) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2376), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002376%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Diagnosing Suboptimal Clustering in Non patterned Flow Cells Video This video highlights which run metrics and thumbnail images to monitor during a run to diagnose overclustering of a non-patterned flow cell.\ < {% embed url="" %} Video length: 8:01 min For further information, see [Cluster Optimization Overview Guide](https://support.illumina.com/downloads/cluster-optimization-overview-guide-1000000071511.html). \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5788), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005788%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Diagnosing Suboptimal Clustering in Patterned Flow Cells Video Although over clustering is not possible on a patterned flow cell, loading a library with a suboptimal concentration negatively impacts run data. In this video, we discuss preventing and diagnosing common clustering issues on patterned flow cells. < {% embed url="" %} Video length: 4:48 min For further information, see [Cluster Optimization Overview Guide](https://support.illumina.com/downloads/cluster-optimization-overview-guide-1000000071511.html).\ \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5789), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005789%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Does my sequencing run look good? Overall sequencing run performance is evaluated by determining whether the sequencing run meets the Illumina specifications for quality scores and data output. Actual run performance will vary based on sample type, quality, and clusters passing filter. Specifications are based on the Illumina [PhiX](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/What-is-the-PhiX-Control-v3-Library-and-what-is-its-function-in-Illumina-Next-Generation-Sequencing-support-bulletin/README.md) control library at [Cluster density guidelines](/instrumentation/general/instrumentation-general-reference_material-list/000001511). **Where can I find instrument specifications?** Follow the links below to the instrument specification pages: [iSeq 100](https://www.illumina.com/systems/sequencing-platforms/iseq/specifications.html) | [MiniSeq](https://www.illumina.com/systems/miniseq/specifications.html) | [MiSeq](http://www.illumina.com/systems/miseq/performance_specifications.html) | [MiSeq i100 Series](https://www.illumina.com/systems/sequencing-platforms/miseq-i100/specifications.html) | [NextSeq 500/550](http://www.illumina.com/systems/nextseq-sequencer/performance-specifications.html) | [NextSeq 1000/2000](https://www.illumina.com/systems/sequencing-platforms/nextseq-1000-2000/specifications.html) | [NovaSeq 6000](https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html) | [NovaSeq X Series](https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html) The [Sequencing Analysis Viewer](http://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html) (SAV) is a free software used to assess the performance of sequencing runs, and can be downloaded from the Illumina website: * SAV v3.0 Supports the NovaSeq X Series, MiSeq i100 Series and NextSeq 1000/2000 XLEAP runs * SAV v2.5.12 Supports NextSeq 1000/2000 on Control Software v1.5 and later with Standard reagents (for XLEAP reagents use SAV v3.0) * SAV v2.4.7 Supports all instruments except Linux based instruments (MiSeq i100 Series, NovaSeq X Series and NextSeq1000/2000) Once SAV is installed, open it and select the tab containing the desired query information. **Note:** SAV 3.0 tabs have different names from previous versions, but with the same information: the Analysis tab (v2.5.12 or earlier) is the same as the Charts tab (v3.0), while the Summary tab (v2.5.12 or earlier) is the same as the Metrics tab (v3.0). **How do I determine if my run meets spec?** Below is an example of a PhiX validation run (2 x 151 bp) on the MiSeq, using v2 reagents. The specifications for this kit (MiSeq v2 300 cycles) are as follows: * Total data output of 4.5-5.1 gigabases (Gb) * At least 80% of bases called with a quality score of 30 or higher (at least 80% ≥ Q30) To determine the quality score, review the Analysis tab Q score Distribution chart and the Summary tab as shown below. -Analysis Tab (Charts tab in SAV 3.0): ![](/files/drSw2mjStYLlVb1tAShy) -Summary Tab (Metrics tab in SAV 3.0): ![](/files/KJrrxBjhpmyWOhj6g9RL) ![](/files/CUEGJlapgNX4dmyLMsAk) The run had a total **Q30** of 94.09% with a total **yield** of 6.10 Gb and meets quality specification for this kit (Q30 ≥ 80%; yield >4.4 Gb). **What additional information can I obtain from SAV?** The following images are from [BaseSpace public data set](https://basespace.illumina.com/datacentral): “MiSeq: Nextera DNA Flex (replicates of *E. coli, B. cereus*, and *R. sphaeroides*)”. Note: Nextera DNA Flex has been renamed to [Illumina DNA Prep](https://support.illumina.com/sequencing/sequencing_kits/illumina-dna-prep/documentation.html). ![](/files/h6iu7aIDngOxb17VKgHU) **Figure 1.** Analysis Tab: Overview of the run metrics. 1. Flow Cell Chart shows color-coded metrics per tile for the entire flow cell. 2. Data by Cycle displays various metrics for each cycle of the run. Select the displayed metric, lane, surface, and channel using the drop-down lists. 3. Q Score Distribution shows a quick overview of the quality of the run. The Q30 for the whole run is found in the upper right of this box. 4. Data by Lane shows plots of metrics per lane. 5. Q score Heatmap displays a heat map for Q score by cycle. ![](/files/pe8a4RxbpzrDssemGoVv) **Figure 2.** Imaging Tab: Displays thumbnails from the run if available. 1. Toggle which base or color channel image to view here. 2. If thumbnails are saved for the run, they are displayed here. ![](/files/NtwjM72HNnjOSnqba6MF) **Figure 3.** Summary Tab: Provides basic data quality metrics summarized per lane and per read. 1. Run summary per read, including quality, is reported here. 2. More details per read including the exact density, clusters Passing Filter (PF), and % aligned. ![](/files/Z0E6WwKVNpOJ3QEUMqcE) **Figure 4.** Indexing Tab: Total and Per Sample % Reads Identified if a sample sheet was used and demultiplexing was performed. 1. Metrics for the entire run. Note: % Reads Identified will not include any PhiX because PhiX is not indexed. 2. Metrics per sample, using indexing information from the sample sheet. 3. Graph plotting the percent of reads identified for each sample present in the sample sheet. **Additional Resources:** * * [Sequencing Analysis Viewer Software Guide](https://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav/documentation.html) * [Sequencing Analysis Viewer (SAV) Training](https://support.illumina.com/content/dam/illumina-support/courses/sav-overview/story_html5.html) * [Plotting %Occupied by %PF to optimize loading for the NovaSeq 6000 and X, MiSeq i100, and iSeq 100](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Plotting-Occupied-by-Pass-Filter-to-optimize-loading-concentration-for-NovaSeq-and-iSeq-100-platforms-support-bulletin/README.md) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1922), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002308%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # End of Life (EOL) Sale and Support of the MiSeq RUO, MiniSeq and iSeq 100 Systems and Consumables **Background** Illumina announced the end of life (EOL) that includes the sale and support for the MiSeq RUO system, certified pre-owned MiSeq RUO system, MiniSeq system, iSeq 100 system, and associated consumables in a Product Obsolescence Notification (PON) sent to customers on **27-MAR-2025**. This PON was distributed to North, Central, and South America, Europe, Africa, Middle East, and parts of Asia. **Key Dates** EOL Announcement: **27-MAR-2025** Instrument End of Sale (EOS): **30-SEP-2025** Consumable EOS: **2H 2029 (second half of the year; specific date to be determined in 2029)** Final EOL: **31-DEC-2029** **Important Dates about Service Contracts** New or lapsed Service Contracts **must** be renewed by EOS on **30-SEP-2025**. * * Instruments that are OFF contract after this date will NOT be eligible for renewal. * If a Service Contract is not renewed each year between EOS on **30-SEP-2025** and EOL on **31-DEC-2029**, the user will NOT be able to purchase a new Service Contract. * Service Contracts renewed AFTER **31-DEC-2028** will still end **31-DEC-2029**, with Service Contracts being prorated for shortened service period. For questions about service contracts, see the [Instrument Service Plans](https://www.illumina.com/services/instrument-services/service-plans.html) page. **Note about replacement parts**, **hardware**, **and consumables** Illumina will provide a best effort to provide spare or replacement parts for hardware until **31-DEC-2029**, though Illumina cannot guarantee availability or lead times for parts or Advanced Exchange units. * Certain reagent kits may be discontinued earlier than the second half of 2029 if demand remains low. Contact [Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) to request the full Product Obsolescence Notification and FAQs. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #9536), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009536%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # End to end sequencing and microarray training at Illumina Solutions Centers in the Americas Illumina has Illumina Solution Centers world-wide, and offers end-to-end trainings for both sequencing and microarray workflows. The interactive catalog [here](https://illumina.pagetiger.com/amr-complete-solutions-for-customers) reviews the complete catalog of Illumina's End-to-End Service and Support Solutions offerings along with information on how to request trainings at Illumina Solutions Centers in the Americas. This content can also be viewed by scanning the QR code below. ![](/files/nqTsROH5ODXa89aa5nhv) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8977), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008977%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Features of Illumina Advantage (IA former TG) product Illumina Advantage (IA, formerly TG Translational Genomics) large-scale sequencing products feature lot-specific shipments and testing, extended shelf life, and advanced change notifications for greater laboratory efficiency. ![](/files/gPlMNIXJZHnK7JOKPtJs) For more information, see the [Support Page](https://www.illumina.com/clinical/large-scale-sequencing-products.html). \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5173), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005173%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Focus images on the MiniSeq and NextSeq 500/550 **Background** At the beginning of Read 1 on the MiniSeq and NextSeq 500/550, the instrument determines the best Z position (distance between the objectives and flow cell) where the clusters are well-focused. During this process, the instrument takes and saves a series of Focus Images. Many of the images are black with a laser dot and contain in the file name nomenclature, "Laser\_AF\_zpos... method\_AutoFocus". These images are laser only and thus clusters are not excited and not seen. However, some focus images show clusters and have in the file name nomenclature, "Red\_IM\_zpos... method\_AutoFocus\_BestFocus". These images show visible clusters when the Z position is correct, allowing for proper focus of the clusters on the flow cell. Technical Support can evaluate Focus Images to diagnose clustering issues (failed to cluster/ underclustering and overclustering) or an unstable focus model. **Location of Focus Images:** * MiniSeq: D:\Illumina\MiniSeq Sequencing Temp\[Run Folder]\Images\Focus * NextSeq 500/550: D:\Illumina\NextSeq Control Software Temp\[Run\_Folder]\Images\Focus **Example Focus Images:** | **Clustering** | **Phenotype** | **Example Image** | | ------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------- | |

Normal cluster density
\~220 k/mm2

| Standard clustering | ![rtaImage (1).jfif](/files/ew8cbZDb540qqxOOmuZ4) | | Ultra low cluster density |

All cameras disabled
at cycle 1

Visible background between clusters

White edges due to increased intensity

| ![Ultra Low Density.jfif](/files/yQciTZJj2ZfivYvFXtTg) | | Very low cluster density |

All cameras disabled
at cycle 1

Visible background between clusters

| ![Very low cluster density.jfif](/files/9G0VyTHo84O73O2vDvAF) | | Low cluster density |

Low intensity or high G base calling

Visible background between clusters

No white edges

| ![Low cluster density.jfif](/files/021JtbNKpXjA9TnFwx8M) | | High cluster density |

No white edges

Visible fold-like artifacts

|

High cluster density 1.jfif
High cluster density 2.jfif

| | No clusters | White edges indicate increased intensity to compensate for initial lack of clusters | ![No clusters.jfif](/files/6fcI0DpgX0ZHKXKAFJhV) | \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6325), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006325%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Hard drives and computer information of the MiniSeq This is a list of general hardware and software information for the MiniSeq: * Hard drive: 1 Tb * C drive: 250 Gb * D drive: 750 Gb * In general, there is enough space for around 45 runs worth of data. * 5-6 Gb of space is needed for a 300 cycle run. * 10 Gb of additional space is needed for analysis files when using the Local Run Manager Resequencing module. * Some analyses need scratch space (temporary storage) for analysis to complete. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2013), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002013%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Heat output specifications for Illumina sequencers The following table details the thermal output and power rating for Illumina sequencers. More information is available in the Site Prep guide for each respective instrument. ![](/files/y5EtVUjjUAxRLXbejgrt) \*Excludes UPS (uninterrupted power supply) output. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8388), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008388%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How Do I Prepare for My Illumina Instrument Delivery? Video This video discusses what to expect during the pre-installation, shipping, and delivery stages of instrument delivery. It also highlights important steps in the process and introduces available resources. < {% embed url="" %} Video length: 7:13 min **Note:** Depending on the region, the steps shown in this video may not apply to the iSeq 100 System. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5767), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005767%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How To Power Cycle NovaSeq 6000 Video This video describes how to power cycle the NovaSeq 6000. Power cycling the NovaSeq 6000 is recommended for troubleshooting only and not recommended for general maintenance. For more information about instrument maintenance, see the [NovaSeq 6000 Sequencing System Guide](https://support.illumina.com/sequencing/sequencing_instruments/novaseq-6000/documentation.html) . < {% embed url="" %} Video length: 1:00 min This information is also available in written form. For further information, see Knowledge Base article [How to Power Cycle the NovaSeq 6000](/instrumentation/general/instrumentation-general-reference_material-list/000002470) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5611), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002470%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How many cycles of SBS chemistry are in my kit? Ensuring sufficient volumes of SBS reagents are loaded onto the sequencing instrument is crucial for a successful run. Running out of reagents during a run impacts intensity and quality metrics, and can result in total run failure. Dual-index sequencing follows different workflows depending on the instrument, as discussed in the [Indexed Sequencing Overview Guide](https://emea.support.illumina.com/downloads/indexed-sequencing-overview-15057455.html). On MiniSeq with Rapid kit and MiSeq instruments, dual-index runs require an additional seven cycles of reagents for the chemistry-only cycles at the beginning of the second Index Read. The seven chemistry-only cycles are required for the workflows in which the second Index Read sequencing occurs after the forward template anneals to the grafted P5 primer on the surface of the flow cell. These seven cycles must be considered when calculating the number of cycles supported by the kit. The following table outlines available reagent kit sizes and the maximum number of cycles each kit can perform, taking the additional seven cycles into consideration when necessary: ![](/files/2TltJXsnXwX55O80AEbV) \*The NextSeq 1000/2000 P2 v3 300 cycle kit has 338 total cycles while the P3 v3 300 cycle kit has 327 total cycles. \*\*All the NextSeq 1000/2000 XLEAP kits have 38 extra cycles. For details on maximum supported cycles in each read, refer to the article [Maximum read length for Illumina sequencing platforms](/instrumentation/general/instrumentation-general-reference_material-list/000002826). \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7002), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002826%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How much PhiX spike in is recommended when sequencing low diversity libraries on Illumina platforms? When sequencing libraries with low base diversity, unbalanced nucleotide composition can negatively impact cluster mapping (on non-patterned flow cells) and template registration (on patterned flow cells) along with data quality and data output. For more information on the importance of base diversity on Illumina sequencing platforms, refer to [What is nucleotide diversity and why is it important?](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/What-is-nucleotide-diversity-and-why-is-it-important-support-bulletin/README.md) To compensate for low base diversity in libraries, Illumina recommends spiking in the PhiX Control v3 Library (catalog number [FC-110-3001](http://www.illumina.com/products/phix_control_v3.html), commonly referred to as "PhiX") for sequencing. The PhiX Control v3 Library has a diverse base composition (45% GC and 55% AT) that provides the balanced fluorescent signals that low diversity sample libraries lack during each sequencing cycle. This, in turn, assists with cluster mapping/template registration and improves overall run performance. For more information about using PhiX Control v3 Library, refer to the article [What is the PhiX Control v3 Library and what is its function in Illumina Next Generation Sequencing](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/What-is-the-PhiX-Control-v3-Library-and-what-is-its-function-in-Illumina-Next-Generation-Sequencing-support-bulletin/README.md) This table lists the percentage of PhiX Control v3 library Illumina recommends spiking in when running low diversity libraries on the indicated sequencing platforms and control software versions. \| **Platform** | **PhiX Aligned (%)†** |\ \| iSeq 100 | Minimum 5% |\ \| MiniSeq | 10-50%\* |\ \| MiSeq (MCS 2.2 or higher) | Minimum 5% |\ \| MiSeq i100 Series | Minimum 5%\*\* |\ \| NextSeq 500/550 | 10-50%\* |\ \| NextSeq 1000/2000 | 10-50%\*\*\* |\ \| NovaSeq 6000 | Minimum 5% |\ \| NovaSeq X Series (Control Software version ≤ 1.2) | 10-20% |\ \| NovaSeq X Series (Control Software version 1.3) | Minimum 5% | † Differences in clustering efficiency between PhiX and the sample library can affect the PhiX spike-in percentage required to achieve the above-targeted percent PhiX aligned. For example, more PhiX may be required if the sample library clusters more efficiently than PhiX. Contact Technical Support at with any questions about a particular library and platform. \*PhiX can be further adjusted based on experimentation. Illumina recommends starting with higher spike-in percentages and reducing based on run performance. \*\* For MiSeq i100 runs exceeding 2 x 350 cycles, use the [PhiX Indexed Control (1000 Cycle) Product Information](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/PhiX-Long-Read-Formulation/README.md) (catalog number [20151542](https://www.illumina.com/products/by-type/sequencing-kits/cluster-gen-sequencing-reagents/phix-control-v3.html#tabgroup-1-tab1)). \*\*\* For low diversity libraries using NextSeq 1000/2000 Standard P1 and P2 600 cycle kits, at least 32% of reads should align to PhiX for optimal performance. Illumina recommends spiking in 40% to account for potential variation in final % read alignment metric. Depending on the type of low diversity library, this may be reduced after optimization. With XLEAP-SBS 600 cycle kits, there is higher performance when compared to the Standard long read kits, especially at the end of the reads. The below XLEAP results are based on testing performed with P2 XLEAP-SBS 600 cycle kits. ![](/files/AFpXokJUaTCVKOKGRbft) Frequently Asked Questions: * Can the PhiX Control v3 Library provide improved nucleotide diversity for low diversity index sequences? * No, the PhiX Control v3 Library is unindexed and does not balance signals in index reads. * Are there other considerations when sequencing low diversity libraries on non-patterned flow cells? * Yes. Reduce the library loading concentration to target a cluster density 30-40% below the optimal range for the chemistry version and platform used. The optimal amount of reduction required must be empirically determined. For more information, refer to the following resources.\ \- [Cluster density guidelines for Illumina sequencing platforms using non-patterned flow cells](/instrumentation/general/instrumentation-general-reference_material-list/000001511)\ \- [Optimizing Cluster Density on Illumina Sequencing Systems](http://support.illumina.com/content/dam/illumina-marketing/documents/products/other/miseq-overclustering-primer-770-2014-038.pdf) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1527), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001511%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Clean Illumina Sequencer Wash Cartridges Video This video shows how to clean and maintain wash cartridges/trays for Illumina sequencers to prevent contamination. < {% embed url="" %} Video length: 4:41 min \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6608), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006608%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Create a Sample Sheet in Local Run Manager Sample sheets are created through Local Run Manager (LRM) for MiSeq (MiSeq Control Software v3.1 and later), NextSeq 500/550, MiniSeq and iSeq 100. **Considerations:** * Illumina recommends creating the sample sheet **prior** to preparing sample libraries. * Before starting the run, make sure the sample sheet is accessible to the instrument. * Copy the sample sheet to a network location accessible to the instrument or transfer via a USB drive onto the instrument.\ \- If copying from network or USB drive, it is best practice to store the file locally and reference the local file location during run setup. * When the run begins, the software copies the sample sheet from the designated sample sheet folder to the root of the Output folder. At the end of the run, the sample sheet is used for secondary analysis performed by LRM. **Follow the instructions below to create a sample sheet:** 1. Connect to LRM via a Chromium web browser using the domain 1. If prompted, login to LRM 2. Select **Create Run** 3. Select the desired workflow (For example: **GenerateFASTQ**) * ![](/files/oKsxQdRHZAaf3F5JR8GY) 4. Enter the desired **Run Name** 5. Select the desired **Library Prep Kit** from the drop-down menu * If using a non-Illumina library prep kit or a kit type that is not listed, select 'Custom' 6. Select the desired **Index Kit** from the drop-down menu * If using a non-Illumina library prep kit or a kit type that is not listed, select 'Custom' 7. Select the number of **Index Reads** (0, 1, or 2) 8. Select the **Read Type** (Single Read or Paired End) 9. Enter the desired **Read Lengths** for Read 1 and Read 2 * **Note:** The Read Lengths for the Index reads auto-populate based on the number of bases entered into the index columns in the sample sheet. * If selecting a specific kit from the drop-down menu, the index lengths are auto populated based on predetermined settings of the kit. 10. Enter the desired number of rows needed and select the '**+**' symbol to add the rows for the appropriate number of samples * In the example screenshot below, 17 rows are added for a total of 18 rows. 11. Enter the sample names into the **Sample ID** column by either copying and pasting from an excel file or entering each sample name individually * If also using BaseSpace, Illumina recommends using unique sample IDs to avoid potential data aggregation during downstream analyses * Sample ID cannot contain spaces and the following characters: # - ? ( ) \[ ] \ / = + < > : ; “ ‘ , \* ^ | & 12. Enter the appropriate indexes * If using a specific kit from the drop-down menu, the indexes can be selected from the drop-down menu. * Alternatively, if the indexes (or well numbers) are stored in an excel file, that column can be copied and pasted into LRM OR selected by hand. * For example, if a previously created sample sheet lists out well A01-H12, the well IDs can be copied and pasted directly into LRM and the associated indexes will populate accordingly. 13. Select **Export Sample Sheet** and/or **Save Run** ![](/files/U7FWIvR062fbFbMQOHDU) The sections listed below are "optional settings" that may be entered but are *not* required by the software to complete run setup: 1. **Run Description** * Enter a run description if desired 2. **Sample Description** * Enter a sample description if desired 3. **Sample Project** * Enter the desired project name here for samples to be associated with said project once demultiplexing completes on BaseSpace 4. **Module-Specific/Advanced Settings** * For example, adapter trimming settings can be entered here if a custom kit is used. * Note: If using a kit from the drop-down menu, the adapter trimming settings for that kit will be applied automatically and do not need to be entered by the user For additional information, see the [Local Run Manager Software Guide](https://support.illumina.com/sequencing/sequencing_software/local-run-manager/documentation.html) and contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/) if additional assistance is needed. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8106), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008106%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Disable Cloud Login Feature on the MiSeq i100 and NovaSeq X Series **Background** The MiSeq i100 and NovaSeq X Series instruments require users login to the Control Software using either a Local or Cloud login. If the instrument is not connected to the internet and the Cloud login is not required, use the following steps to disable the Cloud login feature and only use the Local login. The Cloud login should only be disabled if the instrument is completely disconnected from an internet connection. This procedure disables all Cloud upload features including both Proactive and BaseSpace features. For more information on Proactive, see the following resources: [Illumina Proactive - Instrument Services](https://www.illumina.com/services/instrument-services/instrument-monitoring.html) [Proactive connectivity guide for Miseqâ„¢ i100 Series](https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/proactive-connect-guide-miseqi100-m-gl-03317/proactive-connect-guide-miseqi100-m-gl-03317.pdf) [Proactive connectivity guide for NovaSeq X Series](https://www.illumina.com/content/dam/illumina/gcs/assembled-assets/marketing-literature/proactive-connect-guide-novaseqx-m-gl-03319/proactive-connect-guide-novaseqx-m-gl-03319.pdf) **Instructions** *Disabling Cloud Login* 1. Ensure the instrument is idle and there are no Active sequencing Runs or DRAGEN Analyses. 2. Log into the instrument as an **Administrator** account. 3. Access the **Settings Menu**: 1. On the *MiSeq i100 Series* Control Software Home screen, select the **dropdown menu** in the top-left corner, then select **Settings**. 2. On the *NovaSeq X Series* Control Software Home screen, select the **instrument icon,** then select **Settings**. 4. Select **Cloud Settings**. 5. De-select all checkboxes under **Run settings** and **Illumina Proactive**. 6. Remove any entries in the **Private domain name** field. 7. Within the **Hosting Location** dropdown menu, select the **blank entry** above the BSSH USA (N. Virginia) selection (**Figure 1**). 1. The Hosting location selection should be empty after selection (**Figure 2**). 8. Select **Save**. ![](/files/uEJP0jozFY0z8KPLPE2N) **Figure 1.** Selection of the empty Hosting location within the dropdown menu. ![](/files/iCydJ8D8QsAD7USvB14b) **Figure 2.** Highlighting the empty Hosting location selection. If the Cloud Settings menu presents the message "An unexpected error has occurred. Details: Internal Server Error," see the following steps: 1. Navigate to the **Cloud Settings** menu. 2. Confirm that all checkboxes are de-selected and the Hosting Location is blank. 3. Select **Save**, then wait 2 minutes. It is expected to display a 'loading circle' that does not resolve. 4. After 2 minutes, select the **X** in the top-right corner of the Cloud Settings UI. 5. Navigate back to the **Home** screen, then select the **dropdown menu** in the top-left corner and then **sign out** of the Admin account. 6. Click the screen to initiate Control Software login and confirm if Local Login presents as the default option. *Re-enabling Cloud Login* 1. Ensure the instrument is idle and there are no Active sequencing Runs or DRAGEN Analyses. 2. Login to the instrument as an **Administrator** account. 3. Access the **Settings Menu**: 1. On the *MiSeq i100 Series* Control Software Home screen, select the **dropdown menu** in the top-left corner, then select **Settings**. 2. On the *NovaSeq X Series* Control Software Home screen, select the **instrument icon,** then select **Settings**. 4. Select **Cloud Settings**. 5. Select the appropriate regional **Hosting Location** using the dropdown menu. 6. For Enterprise users, input the **Private domain name** in the free text field. 7. Select the desired checkboxes under **Run settings** and **Illumina Proactive**. 1. Illumina Proactive - Uploads hardware and run performance data to Illumina Support for troubleshooting purposes. 2. Cloud run monitoring - Uploads run metrics to BaseSpace for user run monitoring. 3. Cloud run storage - Uploads run metrics and data to BaseSpace, required for Cloud Analysis. 8. Select **Test Configuration** and confirm all required URLs are reachable. 1. Consult the local IT team to add the affected URLs to local network security allow list if any URLs are not reachable. 9. If **Test Configuration** is PASS, select **Save**. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #9462), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009462%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Enable/Disable Illumina Proactive on the MiSeq Enable Illumina Proactive on the MiSeq. By connecting MiSeq instrument to Illumina Proactive, Illumina will be alerted to failure risks before they affect a run. Illumina's Service and Support team analyzes instrument performance data, troubleshoots as needed, and schedules any required maintenance. See below how to enable Illumina Proactive on the MiSeq Software: **MiSeq Control Software (MCS) v3.1 or below:** 1. From the Home Screen, select Run Options.\ ![](/files/HmmWDtKsXKufVTH8gOaV) 2. Select **Send Instrument Performance Data** to Illumina from the Run Settings tab (in some MCS versions, the option may be located in the BaseSpace Settings tab).\ ![](/files/viHkNtzrp7cMq41lUlBL) **Note**: To monitor the chiller temperature through Illumina Proactive, MiSeq Control Software 3.1 or greater must be installed. To disable ProActive, de-select **Send Instrument Performance Data to Illumina** in the same tab. **MiSeq Control Software v4.0 or above:** 1. From the Home Screen, select **System Settings**.\ ![](/files/NCkYx1GjOBaGUwJmHjCn) 2. Under the BaseSpace tab, enable the option **Turn on Illumina Proactive Support**.\ ![](/files/x5GBAx5Pa9WJr8Uw5R6r) To disable ProActive, de-select **Turn on Illumina ProActive Support** in the same tab. **Additional Resources:** [Illumina Proactive Webpage](https://www.illumina.com/services/instrument-services-training/product-support-services/instrument-monitoring.html)\ [Illumina Proactive Frequently Asked Questions](https://www.illumina.com/content/dam/illumina-marketing/documents/products/other/illumina-proactive-faq-c-970-2019-004.pdf)\ [Illumina Product Security Portal](https://support.illumina.com/product-security-portal.html) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2412), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002412%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Enable/Disable Illumina Proactive on the NovaSeq 6000 By connecting NovaSeq 6000 instrument to Illumina Proactive, Illumina will be alerted to failure risks before they affect a run. Illumina's Service and Support team analyzes instrument performance data, troubleshoots as needed, and schedules any required maintenance. **To enable Illumina Proactive on the NovaSeq 6000 Software:** 1. From the Home Screen, select the menu button in the upper left corner. ![](/files/OsB4IYD8917oxAX2y6qc) 2. Select **Settings**. 3. Under Settings, select **Send Instrument Performance Data** **to Illumina** from the Run Settings tab. To disable ProActive, de-select **Send Instrument Performance Data to Illumina** in the same tab. ![](/files/xv86dsZyGp6sBTw2PNp0) **Additional Resources:** [Illumina Proactive Webpage](https://www.illumina.com/services/instrument-services-training/product-support-services/instrument-monitoring.html)\ [Illumina Proactive Frequently Asked Questions](https://www.illumina.com/content/dam/illumina-marketing/documents/products/other/illumina-proactive-faq-c-970-2019-004.pdf)\ [Illumina Product Security Portal](https://support.illumina.com/product-security-portal.html) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8507), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008507%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Export Logs on the MiSeq i100 and NovaSeq X Series Instruments **Background** The Export Logs workflow automatically collects relevant logs from the instrument and bundles them into a compressed file that is then transferred to the selected output folder. This feature is only available on NovaSeq X Series Control Software v1.4 and above, and all Control Software versions for the MiSeq i100 Series. This workflow requires that an External Storage has been configured and a default output folder has been selected on that External Storage. If this process has not completed, see the following Product Documentation for additional details: * [NovaSeq X Series Product Documentation - Specify the Default Output Folder Location](https://support-docs.illumina.com/IN/NovaSeqX/Content/SpecifyOutputFolder.htm) * [MiSeq i100 Series Product Documentation - External Storage](https://support-docs.illumina.com/IN/MiSeqi100Series/Content/IN/MiSeqi100/SysOutFolder.htm) **NovaSeq X Series** 1. From the Control Software Home screen, select the **instrument icon** in the bottom-middle and then select **Settings**. 2. Select **Export Logs**. 3. The Standard Log bundle is always included in the Export Logs. 1. If specifically requested by Illumina Support, select additional logs options for Illumina Run Manager or DRAGEN logs as needed. 2. If needed, select checkboxes to include Sequencing Run logs and metrics files. 4. Select **Next**. 5. Use the dropdown menu to select the intended output folder on **External Storage**, then select **Export**. 6. The log exporter then collects and compresses the logs, then transfers them to the selected output folder location. 1. This process can take up to 20 minutes depending on the size of the logs. 7. Once completed, the compressed logs are located in the selected output folder on the External Storage so they can be provided to Illumina Tech Support. **MiSeq i100 Series** *For Control Software v1.1 and above:* * When Exporting Logs, only select **Illumina Run Manager** or **DRAGEN** Logs options when requested by Illumina Tech Support. If needed, select the appropriate Sequencing Runs to include sequencing run logs in addition to the instrument logs. ![](/files/XP5SvxORcfZdiZEJx94S) *For Control Software version 1.0.1 and below:* * When Exporting Logs, select the appropriate **Small**, **Medium**, or **Large** options based on the recommendation from Illumina Tech Support. If needed, select the appropriate sequencing runs to include sequencing run logs in addition to the instrument logs. **Export Logs Workflow** 1. From the Control Software Home screen, select the dropdown menu in the top-left corner and then select **Settings**. 2. Select **Export Logs**. 3. Select additional logs options as appropriate: 1. For *Control Software v1.1* and above: Select Illumina Run Manager or DRAGEN logs only if requested. 2. For *Control Software v1.0.1* and below: Select Small, Medium, or Large logs as recommended. 4. Select **Next**. 5. Use the dropdown menu to select the intended output folder on **External Storage**, then select **Export**. 6. The log exporter then collects and compresses the logs, then transfers them to the selected output folder location. 1. This process can take up to 20 minutes depending on the size of the logs. 7. Once completed, the compressed logs are located in the selected output folder on the External Storage so they can be provided to Illumina Tech Support. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #9265), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009265%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Perform Washes on the MiSeq Video This video demonstrates how to perform washes on the MiSeq, including the post-run wash, the optional template-line wash, the maintenance wash, and the standby wash. < {% embed url="" %} Video length: 8:43 min This information is also available in written form. For further information, see the Knowledge Base article [Best Practices for Washes on the MiSeq](/instrumentation/general/instrumentation-general-reference_material-list/000001679). \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6958), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001679%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Power Cycle the NextSeq 500/550 **NextSeq 500/550 Power Cycle Instructions** 1. From the instrument home screen, select **Manage Instrument.** 2. Select **Shutdown Options.** 3. Select **Shutdown** (this shuts down software and turns off instrument power). 4. Wait two minutes before turning on the instrument from the button in front. 5. Wait for software initialization to return to the Home Screen. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1972), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001972%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Power Cycle the NovaSeq 6000 Illumina recommends power cycling, if needed, during troubleshooting. Regular weekly power cycles are not required on the NovaSeq 6000. To power cycle the NovaSeq 6000, use the following steps. 1. From the main menu of the NovaSeq Control Software, select **Shutdown Instrument**.\ 2\. After the screen goes blank, switch the toggle power switch on the back of the instrument to the off position.\ 3\. Wait 1-2 minutes.\ 4\. Use the toggle switch to turn the instrument ON.\ 5\. Wait for the power button to start to pulse; this can take a few seconds.\ 6\. Use the power button on the right front side of the instrument to turn the instrument computer ON.\ 7\. Log in to Windows.\ 8\. Wait for Windows to load, then select the NovaSeq Control Software icon to initialize the instrument. This information is also available in video at [How To Power Cycle NovaSeq 6000 Video](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/How-To-Power-Cycle-NovaSeq-6000-video/README.md) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2470), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005611%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to Requeue an Analysis on BaseSpace Sequence Hub When No Changes to the Sample Sheet are Needed Analyses for runs using a v1 sample sheet can be requeued through the BaseSpace Sequence Hub (BSSH) Web Interface the majority of the time. Instruments that typically use a v1 sample sheet include the iSeq 100, MiniSeq (updated to Control Software 2 and Windows 10), MiSeq, HiSeq 1000/1500/2000/2500, NextSeq 500/550 (updated to NextSeq 500/550 Control Software 4 and Windows 10), and NovaSeq 6000. Illumina recommends using the Local Run Manager software to create sample sheets, as it guides users through the process and will check for errors. In some instances, an analysis errors out due to communications issues on BaseSpace. If an analysis needs to be requeued using the same sample sheet, follow the instructions below. **Note:** Runs that use a v2 sample sheet (for example the NextSeq 1000/2000) must be requeued with the BCL Convert app on BaseSpace and cannot be requeued through the method described below. **Important Notes:** * MiniSeq and NextSeq 500/550 runs set up using the BaseSpace Sequence Hub PrepTab require different steps to edit run setup and [requeue an analysis](https://support.illumina.com/bulletins/2017/10/how-to-edit-sample-indexes-in-basespace-sequence-hub-preptab-.html). * Only the owner of the run can requeue an analysis. It is possible to [transfer ownership](https://help.basespace.illumina.com/manage-data/transfer-ownership) of a run, if necessary. A [shared run](https://help.basespace.illumina.com/articles/tutorials/share-data-using-getlink/) does not provide the necessary permissions needed to requeue analysis. * There is a limit of five requeue attempts for users of BaseSpace Sequence Hub. If assistance with additional requeues is needed, email [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) and share the run ID and sample sheet. To find the run ID, open the run in BaseSpace, and look in the web browser address bar for the numerical value after: [https://basespace.illumina.com/runs/](https://basespace.illumina.com/runs/active) **To requeue the analysis using the same sample sheet:** 1. After logging in to the BaseSpace account, select the **RUNS** tab at the top of the page. 2. Select the blue hyperlink of the run to requeue. 3. Select the **hourglass** icon below the run name, then **REQUEUE** > **SAMPLE SHEET**. * ![](/files/7KD8CtP41Galu30l1CnY) 4. The sample sheet may be pre-populated in the editing window. If not, select 'Load Original' to load the sample sheet. 5. Once the sample sheet has been validated, select the blue **Queue Analysis** button. * If the **Queue Analysis** button is not active, check for and resolve any validation errors. 6. The status on the run summary page will display "Analyzing" when the analysis is ongoing and will change to "Complete" when the requeued analysis is complete. If reformatting of the sample sheet is required prior to requeueing the analysis, search for Knowledge Base article **How to edit a sample sheet and requeue an analysis in BaseSpace Sequence Hub**. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8380), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008380%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to achieve more consistent cluster density on Illumina sequencing platforms Achieving optimal cluster density is critical to high-quality sequencing on MiniSeq, MiSeq, and NextSeq 500/550. On non-patterned flow cells, cluster density has a significant impact on run performance, specifically data quality and total data output. While underclustering can maintain high data quality, it results in lower data output. Alternatively, overclustering can lead to run failure, poor run performance, lower Q30 scores, introduction of sequencing artifacts, and lower total data output. This article summarizes the resources and best practices to avoid underclustering and overclustering, and to achieve more consistent cluster densities. * Quality check and accurate quantification of libraries is critical. If not performed, it is the most common cause of inconsistent cluster density. Always follow methods listed in the [Library quantification and quality control quick reference guide](/library-preparation/general-library-prep/library-preparation-general-library-prep-reference_material-list/000001247) article to check Illumina libraries. * Follow the latest instrument-specific guidelines to dilute and denature libraries: * [NextSeq 500/550 Denature and Dilute Protocol Generator](https://support-docs.illumina.com/IN/dnd-wizard/Content/dnd/landing.htm?ins=nextseq550) * [MiSeq Denature and Dilute Protocol Generator](https://support-docs.illumina.com/IN/dnd-wizard/Content/dnd/landing.htm?ins=miseq) * [MiniSeq System Denature and Dilute Libraries Guide](https://support.illumina.com/downloads/miniseq-denature-dilute-libraries-guide.html) * Best practices for library denaturation: * The NaOH stock solution must have a pH >12.5 prior to any dilution. Check the pH of the stock solution before diluting. The recommended stock concentration is found in the appropriate instrument system guide or denature and dilution guide. * Always prepare freshly diluted NaOH for denaturing libraries at time of use. * To prevent small-volume pipetting errors from affecting the final NaOH concentration, prepare at least 1 ml of freshly diluted NaOH. * For best results, thaw sequencing reagents before denaturing and diluting libraries. For further instructions, see the system guide for the instrument and the article: [How to thaw and store sequencing reagents for optimal performance](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/How-to-thaw-and-store-sequencing-reagents-for-optimal-performance-support-bulletin/README.md)[.](https://support.illumina.com/bulletins/2016/07/how-to-thaw-and-store-sequencing-reagents-for-optimal-performance-.html) * Follow the denature and dilute libraries guide for the instrument.\ \- For the MiSeq series, it is important that the final solution of NaOH is not greater than 1 mM NaOH after diluting with HT1. Greater than 1 mM NaOH inhibits template hybridization efficiency.\ \- When denaturing libraries for NextSeq 500/550 and MiniSeq, use 200 mM Tris-HCl pH 7.0 to ensure that the NaOH is fully hydrolyzed in the final solution. As a result, template hybridization is not affected even when the final NaOH concentration is greater than 1 mM (see NextSeq 500/550 and MiniSeq denature and dilution guides, above). * For highly structured or GC-rich libraries, cluster density consistency improves when the library is heat denatured before loading the pool onto the instrument. This method is optional for other libraries. * After NaOH denaturation of the sequencing library and dilution with HT1 to the final loading concentration, incubate the diluted library at 96°C for 2 minutes using a heat block. * After the heat incubation, invert the tube 1-2 times to mix. * Quickly move the library to an ice water bath for 5 minutes. The quick cooling step helps lock the library in its single stranded form. * Proceed immediately to cluster generation. * Consider the average size of the library. Because the clustering process preferentially amplifies shorter libraries in a mixture of fragments, large libraries tend to cluster less efficiently than smaller libraries. Loading concentration must be optimized for each library type. * Special consideration is needed when sequencing low-diversity libraries to ensure consistent cluster density and good data quality. See knowledge article: [What is nucleotide diversity and why is it important?](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/What-is-nucleotide-diversity-and-why-is-it-important-support-bulletin/README.md) For low diversity sequencing guidelines specific to NextSeq 500/550 and MiniSeq, refer to the knowledge article: [Best practices for low diversity sequencing on the NextSeq 500/550 and MiniSeq systems](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Best-practices-for-low-diversity-sequencing-on-the-NextSeq-500-550-and-MiniSeq-systems-support-bulletin/README.md) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1481), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002882%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to add Illumina to TeamViewer allowlist Companies/sites that use licensed copies of TeamViewer instead of TeamViewer QuickSupport can sometimes have security restrictions preventing Illumina Technical Support from connecting to their instruments via TeamViewer. This article has instructions for adding connections from Illumina to the TeamViewer allowlist to facilitate these screen share connections. The allowlist can be configured to allow remote access to a device only from selected TeamViewer accounts or specific TeamViewer IDs. **Instructions for adding Illumina to TeamViewer allowlist:** 1. In the TeamViewer full version, select **Settings** > **Security** > **Block and Allowlist** > Select **Configure...** 2. A new window will open. Activate the second option, **Allow** **access only for the following partners,** then select **Add.** 3. After selecting **Add**, either choose partners saved on the computers & contacts list, add a whole company (only visible if computer is part of company profile), or add TeamViewer IDs or contacts manually to the allowlist. 4. Select **Manually add contact to your allowlist** and then type `ILLUMINA INC` into the field. * This allows any connections from Illumina's licensed corporate account to connect to this instrument. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #3777), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003777%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to cache credentials for access to Network Storage and verify Read/Write access **Cache Network Storage Credentials** In order to configure a Windows account with persistent access to Network Storage locations, it is necessary to cache the network storage credentials within the Windows account using the following steps. 1. Login to the instrument using the Windows account(s) which will be writing to network storage (typically **sbsuser**). 2. Open **File Explorer** and enter the network output location (in UNC format) into the address bar.\ ![](/files/HWmUMnNHFm3laDQO6b9g) 3. Enter the credentials of the desired user who has access to the desired network storage location into the Windows Security prompt. You may need to work with your IT team for assistance with these credentials. 4. Select **Remember my credentials**, then select **OK**. This will add the network storage credentials to the Windows **Credential Manager.**\ ![](/files/AcgbT8cixDSD9ffigeMb) 5. Open the **Credential Manager** application in Windows. Verify that the credentials entered above have been cached to in the Windows Credentials. **Note**: If these credentials change, the cached credentials must be updated in order to continue output to your network storage. ![](/files/PqzaHRFto6qKmPK1rEG9) **Verify Write access to Network Output Location(s)** 1. In Windows **File Explorer**, right click within the intended Network Output location and select **New** > **Text Document** to create a new document called test.txt. ![](/files/3Gjc4GHASFuiqAxpiz0O) 2. Delete the file just created. 3. If either of the actions above fails, your account does not have write permissions on the Network Output location. Work with your IT team to configure the Network Output location with appropriate permissions. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7828), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007828%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to change the Windows account type from administrator to standard **Note**:this applies to Local Windows accounts (beginning with .\xxx) only. For domain accounts (beginning with DOMAIN\xxx), work with the institutional IT team to change account type. 1. Log in using any administrator account other than the account that will we be modified. 2. Open the **Settings** app. 3. Select **Accounts >** **Family & Other Users**. 4. Select the account of interest (**MyUser** in this example). 5. Select **Change Account Type >** **Standard User**. 6. Select **OK**. ![](/files/eHy4xvSdkWzv3hXh7KTo) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7827), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007827%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to check .NET version on Windows instruments To check the .NET Framework version on instruments running Windows Operating Systems, follow the steps below: 1. Open the Windows file explorer and navigate to C:\Windows\Microsoft.NET\Framework. 2. Open the folder with the highest version (V.x). 3. Right click any of the .dll files and select Properties. 4. Select the **Details** tab; the .NET framework version can be found under File version. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7801), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007801%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to check if a Windows account is a standard or administrator account 1. Open the **Settings** Windows app. ![](/files/Gj9mk2irJOMQr7imI4LB) 2. Select **Accounts**.\ ![](/files/nSC9frybHHqKF81nPgFy) 3. Locate the desired account to check: * **Your Info** - if currently logged in as the user that needs checking. * **Family & Other Users** - if checking a different account than the one currently logged in. ![](/files/ifhoXBD809QKegAzUVbO) 4. Find the account type beneath the account name. * If the account says **Administrator** beneath it, then it is an administrator account. * If the account does **not** say **Administrator** beneath it, then it is a standard account. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7826), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007826%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to collect Group Policy Object (GPO) reports **What are Group Policy Objects (GPOs) and how do they work?** GPOs are a hierarchical infrastructure that allows a network administrator to implement specific configurations for groups of users and computers that are joined to a domain on the network. These security policies ensure computers on a network adhere to common safety practices. However, this can sometimes perform actions such as installing antivirus or security software, restricting programs from running, or removing permissions that can inhibit instrument operation. Running a GPO Report can provide information on what GPOs and Local Policies have been applied to the control computer on Illumina instruments. **How to generate a GPO report** **Important**: GPO Reports **must** be collected from a Command Prompt with elevated permissions. When opening the Command Prompt, select 'Run as Administrator' even if already running as a local Administrator account (this is **required**). To generate a GPO report, see the following instructions: 1. In the Windows Search Bar, type 'cmd' then right-click the App and select '**Run As Administrator**' 1. Enter the sbsadmin credentials if prompted. 2. In the Command Prompt window, type **gpresult /v /r > C:\Illumina\GPO-Result.txt** and press Enter. 3. This will generate a GPO report and output it to a text file in the C:\Illumina folder on the instrument. 4. Check the text file. If the report lists **INFO: The user does not have RSoP data** then force a Group Policy update by typing **gpupdate /force** in the console window, then repeat Step 2. If there are any errors that present when running a GPO report, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support). \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2273), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002273%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to connect benchtop instruments and Local Run Manager to a network location ### **Introduction** Instrument control software contains several different Illumina Windows Services: * Illumina Universal Copy Service * Illumina Local Run Manager Job Service * Illumina Local Run Manager Analysis Service By default, the Illumina Windows Services are configured to **Log On As** a predefined Windows service account called **Local System**. Successful data transfer from the instrument to a network output location requires that the Illumina Windows Services be reconfigured to **Log On As** a different local Windows account. Services are usually reconfigured to **Log On As** the standard local **sbsuser** account, which exists on all instruments. You may also choose to run the services using a different network domain account if needed. Note: The **Illumina Universal Copy Service** must be configured to log on as a standard (non-Administrator) Windows account. ### ### **Prerequisites and Requirements** * The **Log On As** account (typically **sbsuser**) must have read/write access, or cached credentials with read/write access, to the network storage destination. * It must have at least “read only” or “list folder content” permissions to all parent folders within the Universal Naming Convention (UNC) path. * In the example of \server\level1\level2, the account must have at least read-only access to the \server and ..\level1 folders. * Use the full UNC path to the output folder with preceding double backslashes and a trailing slash, such as \server\level1\level2. * Do NOT use a mapped network drive path such as Z:\\ * The network storage destination must have enough storage for the run. The amount of storage needed can vary by flow cell type and instrument. * Reference the article [Approximate sizes of sequencing run output folders](/instrumentation/general/instrumentation-general-reference_material-list/000001508) for estimates. #### **STEP 1: Updating the Illumina Services Log On Accounts** #### **WARNING:** Illumina has updated the guidance for configuring LRM and UCS service accounts and now should be done via the **Windows Services** if using Local Run Manager **v3.x**or via the **Service Accounts** tab directly on Local Run Manager if on **v4.x**. ### *For Instruments running Local Run Manager (LRM) v4.x* 1. Login to Local Run Manager (LRM) as an LRM Administrator account, typically `admin`. 2. In LRM, select **Tools**, then select **System Settings** and then the **Service Accounts** tab. 3. Under the Service Accounts tab, select **Windows Account** for each Service and then input the appropriate user account. 1. If using a local account such as `sbsuser`, input as .\sbsuser and then input the `sbsuser` password. 2. If using a domain account, input as DOMAIN\username, ex. ILMN\johndoe for the `johndoe` account on the `ILMN` domain. ![](/files/BFJr1x2sriIMKMYs0XSH) ![](/files/komBmeB5wJAdYUsLBVNw) *For Instruments running Local Run Manager (LRM) v3.x* 1. Login to the instrument using the sbsadmin account. 2. Search for **Services** in the taskbar and open the app with right-click and **Run as administrator.**\ ![](/files/pmn4PUgcbsAiOdDmm5zF) 3. Enter `sbsadmin` account credentials in the pop-up window if prompted. 4. Locate the three Illumina services. 5. Right-click on **Illumina Universal Copy Service.** 6. Select **Properties** and navigate to the **Log On** tab.\ ![](/files/uWmjNolyAWO3XYF8oTSN) 7. Select **This account** and browse to search for the account. In the **Select User** window, select **Advanced** and then **Find Now.** Select the desired **Log On Account** (generally `sbsuser`) from the search results.\ ![](/files/JgcVokYvLV0ExqIDGcRz) 8. Select **OK** to acknowledge both windows. 9. Enter the password for the selected account (typically `sbsuser`), select **Apply** and **OK**. 10. Restart the service by right-clicking and selecting **Restart**. 11. Repeat steps 4 - 8 for the Local Run Manager (LRM) services below (**Note**: some LRM modules may need to Log On As an Administrator account) * **Illumina Local Run Manager Job Service** * **Illumina Local Run Manager Analysis Service** ### **STEP 2: Cache Network User Credentials in Windows Credential Manager** 1. Log in to the instrument as the **Log On As** account configured above (typically `sbsuser`). 2. Open **File Explorer** and enter the Universal Naming Convention (UNC) path to the network output location into the address bar. ![](/files/K4EnlLMgbRPCgfiq6isE) 3. **IMPORTANT:** Select **Remember my credentials** before inputting the credentials. This adds the network storage credentials to the Windows **Credential Manager**. ![](/files/0OKkrh4lDgQJEv8LwzVF) 4. Enter the username and password for the network user account that has access to the network storage location into the Windows Security prompt. 1. It may be necessary to work with the local/lab IT team for assistance with these credentials. 5. Open the **Credential Manager** application in Windows and verify that the credentials entered above have been cached to in the Windows Credentials. 1. **Note**: If these credentials change, the cached credentials must be updated in order to continue output to your network storage. ![](/files/cnYNjwZjVObdSGadHTCQ) ### **STEP 3: Verify Write Access in the Network Output Location** 1. In Windows **File Explorer**, right click within the intended Network Output location and select **New > Text Document** to create a new document called test.txt. ![](/files/zC6adUZeLsUvuIcJ3SiS) 2. Delete the test.txt file just created. 3. If either of the actions above fails, the account does not have the appropriate permissions on the Network Output location. Work with the local/lab IT team to configure the Network Output location with appropriate permissions. ### **STEP 4: Configure output folder to the network** Instrument Control Software * Set the Output Folder location as full UNC path (with trailing backslash) in the Instrument Control Software. Local Run Manager * Refer to the article [How to requeue and import run data for reanalysis with Local Run Manager](/instrumentation/general/instrumentation-general-reference_material-list/000001324) and the section **To import data to a new analysis module**. Import a run to be able to set the Base Output Folder to the network location. Enter the network location as the full UNC path. ![](/files/kuvuGpkOGL82V47UoYvD) **FAQ** 1. **Changing Windows Account Passwords** If the Windows account passwords change, the credential configurations must be updated by repeating STEP 1 for all **Illumina Windows Services** using the new password. Failure to update the password can cause connectivity issues and failures during sequencing runs. 2. **How to access the full UNC path of a mounted drive** * Launch the Windows Command Prompt app * Enter the command `net use` * This will display the full UNC path to all network drives mounted on the system \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1934), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001324%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to disable and add exceptions to the Software Restriction Policies for TeamViewer in Windows 10 **Background** Instruments with Windows 10 Operating System (OS) have the Software Restriction Policies (SRP) feature enabled by default. This security feature blocks programs that are not specifically on the SRP exceptions list. When using TeamViewer QuickSupport (QS), an exception must be added to SRP to allow TeamViewer QS to launch properly. **Resolution Actions** *Disabling and Enabling SRP* 1. Confirm that a sequencing run is not in progress and the instrument is idle. 2. Log in to the Windows OS using the sbsadmin local Administrator account. 1. For NovaSeq 6000 with serial numbers smaller than A01535, the `sbsuser` account is part of the Administrators group. 3. Open Windows **File Explorer** and navigate to the C:\Illumina\Security folder (Figure 1). 4. Double-click **Disable.reg** and acknowledge the prompts (Figures 2, 3). 5. When finished, double-click **Enable.reg** and acknowledge the prompts to re-enable SRP. *Adding Exceptions for TeamViewer to SRP* 1. Confirm that a sequencing run is not in progress and the instrument is idle. 2. Log in to the **Windows OS** using the sbsadmin local Administrator account. 1. For NovaSeq 6000 with serial numbers smaller than A01535, the `sbsuser` account is part of the Administrators group. 3. Disable SRP by navigating to C:\Illumina\Security, double-clicking **Disable.reg**, then acknowledge the prompts (Figures 1-3). 4. In the Windows search bar, input `secpol` and open the Local Security Policy App (Figure 4). 5. In the **Local Security Policy** dialog box, expand **Software Restriction Policies**, then select **Additional Rules** (Figure 5). 6. To add a rule: 1. On the **Action** menu, select **New Path Rule**…. 2. In the **Path** field, enter the certificate, file name, file extension, or directory that you want to allow. 3. In the **Security level** list, select **Unrestricted**. 4. \[Optional] In the **Description** field, enter a reason for creating the rule. 5. Select **OK** to add the rule. 7. Separately add the following rules using **Steps 6a-e** for both of the following paths (Figures 6, 7): 1. TeamViewerQS\*.exe 2. C:\Users\\*\AppData\Local\Temp\TeamViewer\\* 8. Close the **Local Security Policy** application. 9. Reenable SRP by navigating to C:\Illumina\Security, double-click **Enable.reg**, then acknowledge the prompts. 10. Sign out of `sbsadmin` account and then sign back in as `sbsuser` for the settings to take effect. ![](/files/xEX96jiAzUJAk9ZokAAi) **Figure 1:** Double-click **Disable.reg** to disable SRP. ![](/files/RbQmiVq5HinvPcI8VgE2) **Figure 2**: Select **Yes** to acknowledge the prompt. ![](/files/kiraBTKUiqp39UvnmLzQ) **Figure 3**: Select **OK** to acknowledge the prompt. ![](/files/0w0BTgRfkQfbCXc1wUwy) **Figure 4**: Open **Local Security Policy** to add exceptions for TeamViewer to SRP. ![](/files/mn6EyERcV7czBm0CV0kU) **Figure 5**: Expand **Software Restriction Policies** and then select **Additional Rules**. ![](/files/vX8A3BxyXm99MVZZPID8) **Figure 6**: Select **Action** and then select **New Path Rule**... ![](/files/BsD2Yz2gKQY1Czq1w5sv) **Figure 7**: Input TeamViewerQS.exe in the **Path** free-text field and select **Unrestricted** in the Security Level drop-down menu, then select **OK**. Repeat these steps to add C:\Users\\*\AppData\Local\Temp\TeamViewer\\* as a second Path Rule. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6523), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006523%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to identify the IP and MAC address of a sequencing instrument The Internet Protocol (IP) and Media Access Control (MAC) addresses for an instrument are often used by IT/Networking teams to identify an instrument on the network and assign special security permissions. These will be unique for each Network Interface Card (NIC) on the instrument. Most Illumina instruments have 2-3 NICs available, generally one for external connections to a network and another for the instrument's internal connections. To identify the IP or MAC addresses of a particular instrument, use the Command Line in Windows or the Terminal in Linux. \*\*In Windows Operating System (OS) Environments:\*\*1. In the search bar in the bottom left corner, type in *cmd* and then press enter to open the Command Line interface.\ 2\. In the Command Line, type in ipconfig /all and press enter.\ 3\. The printout will display the IPv4 and Physical Address for each NIC, which are the IP and MAC addresses, respectively. * Many instruments will have internal and external-facing NICs; do not modify or alter the settings for the internal-facing NIC. **In Linux OS Environments:** 1. On the Linux desktop, right-click and select 'Open Terminal'. 2. In the Terminal window, type `ifconfig` and press Enter. 3. The printout will display the configuration settings for each NIC on the instrument. * `inet` = IPv4 Address * `ether` = MAC address 4. For the NextSeq 1000/2000 platforms, there are the following NICs: * Enp2s0: Recommended external NIC * Enp5s0: Internal NIC * Enp6s0: Alternate external NIC \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2222), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002222%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to identify the UNC path of a network server or location. The Universal Naming Convention (UNC) is a standard for identifying servers, printers, and other resources on a network. A UNC network path has the following format: **\servername\share\path** Illumina recommends using the UNC path when setting a network server as the default output location and is a requirement for most Illumina platforms running Windows 10. Use the following steps to identify the UNC path for an existing mapped network location in Windows: 1. In the Windows Search bar, type in `cmd` and press 'Enter' to open the Command Prompt. 2. In the Command Prompt, type `net use` and press 'Enter' to run the command. 3. The output will list the local drive letter under the 'Local' column and UNC path under the 'Remote' column for each network resource that has been mapped to that instrument. ![](/files/3hHKc1GImXofTBM8ZFkC) **Figure 1**: Example output of the `net use` command with the UNC path listed under the 'Remote' column in the output. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2274), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002274%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to import a pre existing index kits into Local Run Manager v3 and v4 In some cases, new index kit offerings will be made available for existing library preparation kits. Index kit files (pre-existing index kit files) can be added to existing Library Prep kit options in Local Run Manager. Use the steps below to import a pre-existing index kit into Local Run Manager (LRM) v3 or v4. 1. Save the desired index kit locally on the instrument. 2. Open Local Run Manager by navigating to via the Chromium Web Browser on the instrument. 3. Select **Tools**. 4. Select **Index & Library Prep Kits**. 5. Select the tab for **Index Kit**. ![](/files/i3aKs0azc51dbCteMWMW) 6. Select **Add Index Kit** on the right-hand side. 7. Browse to the index kit saved on the instrument and select **Open**. For information on creating a custom library prep kits/index kits to import into Local Run Manager v3 and v4, see Knowledge article[How to use custom library prep and index kits with Local Run Manager v3 and v4](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005897). If additional assistance is needed, [contact Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/). \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8929), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000008929%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to install Windows critical security updates on Illumina instruments Illumina encourages customers to apply Illumina-Tested operating system security patches on a regular basis. Illumina tests critical operating system security patches to verify compatibility with Illumina systems running the most recent version of instrument software. Installation instructions and tested updates can be found on [Operating System Security Updates](https://support.illumina.com/support-content/os-patches.html). \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2282), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002282%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to interpret clusters passing filter in run metrics Determining the number of reads passing filter (Reads PF) is critical for evaluating the overall success of a sequencing run. Follow the below instructions for determining the number of clusters passing filter for a single lane, a single read, and a run using BaseSpace Sequence Hub (BSSH) or Sequencing Analysis Viewer (SAV). [**BaseSpace Sequence Hub**](https://basespace.illumina.com/dashboard) **How to access READS PF in the METRICS tab** 1. Select a run. 2. Navigate to the **METRICS** tab. ![](/files/WkKNeE0m32KZ6bOLrdjc) **Figure 1**. Metrics tab in BSSH. 3. Locate the **Per Read Metrics** table. 4. Locate the **READS PF** column. * Values are the calculated number of READS PF per lane. * For a paired-end run, multiply this number by two to calculate the total number of READS PF per lane. 5. To obtain the number of READS PF for the entire run, add the total number of **READS PF** for each lane. ![](/files/sEkpLUjf4JA7qDgwAJaX) **Figure 2**. READS PF values are the calculated number of READS PF per lane. For a paired-end run, multiply this number by two to calculate the total number of READS PF per lane. For example, the NovaSeq run shown here has 2,313125,376 READS PF in Read 1 in lane 1. Because this is a paired-end run, the total number of READS PF in lane 1 is 4,626,250,752. **How to access READS PF in the INDEXING QC tab** 1. Navigate to the **INDEXING QC** tab. 2. Locate the **PF READS** column per lane. * To switch between lanes, use the drop-down menu. 3. To obtain the number of READS PF for the entire run, add the total number of **PF READS** for each lane. **Note**: The **INDEXING QC** metrics are calculated after demultiplexing, and therefore provide a more accurate read count than the metrics tab. ![](/files/b1RRkzXBlSEjrtLNTuzJ) **Figure 3**. In the INDEXING QC tab, total number of reads passing filter are shown per lane. To switch between lanes, use the drop-down menu. [**Sequencing Analysis Viewer**](https://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html) 1. Navigate to the **Summary** (SAV version <3.0)or **Metrics** tab (SAV version 3.0). 2. The **Cluster Count PF (M)** (SAV version <3.0) or **Reads PF(M)** (SAV version 3.0) column shows the number of reads passing filter in millions per lane and per read. 3. To obtain the total number of reads passing filter per read, add the values for a particular read. In this case, Read 1 contains 4,659,600,000 clusters passing filter. ![](/files/O58j9KEoJOdKpyTmQmNu) **Figure 4.** In the **Summary** tab, the **Cluster Count PF (M)** column shows the number of reads passing filter in millions per lane and read. For example, Read 1 of lane 1 contains 2,313,130,000 reads passing filter. To obtain the total number of reads passing filter per read, add values 2,313,130,000 and 2,346,470,000. In this case, Read 1 contains 4,659,600,000 reads passing filter. The total number of reads passing filter for this run is \~9,319,200,000. 4. To determine the total number of reads passing filter for a run, add all the values in the **Cluster Count PF** (SAV version <3.0)or **Rea\*\*\*\*ds PF** (SAV version 3.0) column, excluding non-index reads. * The precise value is in the **Indexing** (SAV version <3.0)or **Indexes** tab (SAV version 3.0) under the **PF Reads** column. ![](/files/9UESqY22uaxtuJkqyBYk) **Figure 5**. Selection pane on SAV for Indexes Passing Filter **Note**: * Values are represented slightly differently in BSSH and SAV. In both programs, the Reads PF tabs represent identical values, as do the Reads PF and Cluster Count PF (M) in the summary tabs. * SAV 3.0 tabs have different names from previous versions, but with the same information. For more information about Sequencing Analysis Viewer or BaseSpace Sequence Hub, visit their respective support pages: * [Sequencing Analysis Viewer](https://support.illumina.com/sequencing/sequencing_software/sequencing_analysis_viewer_sav.html) * [BaseSpace Sequence Hub](https://basespace.illumina.com/dashboard) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6529), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006529%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to invite users to a workgroup on BaseSpace Sequence Hub (Professional or Enterprise tier) BaseSpace Sequence Hub (BSSH) is the Illumina cloud-based platform for data management, storage, and analysis. There are three BaseSpace Sequence Hub subscription tiers - Basic, Professional, and Enterprise. The [Workgroup](http://www.illumina.com/informatics/research/sequencing-data-analysis-management/basespace.html) feature for the Professional and Enterprise tiers gives BaseSpace Sequence Hub users access to pooled resources. A workgroup consists of users who share data, storage space, and other resources. Only the workgroup administrator (admin) can add users to a workgroup, as described in the steps below. 1. Log into BaseSpace Sequence Hub. Switch to the workgroup by selecting the user name in the top right corner and select the workgroup. Select the user name again and select **Settings**. Then select **manage workgroups.**\ ![](/files/aBxgMrF37EJrxuDaUAsB) 2. Select the workgroup to which you want to add users to (ILMN\_TechSupport is the name of the workgroup in this example).\ ![](/files/76Srf6Xy4OG4OhpsvfZh) 3. Select **USERS** on the left panel. Do not use the Invite option on the Administrators screen. The Invite option will invite the user as an admin only. A Professional workgroup can have only one admin.\ ![](/files/wfo2vhFyy8OXgWsNIVqL) 4. Select **Invite**.\ ![](/files/Zb7DMWtZ6VGCGIvYCGKd) 5. Add the BaseSpace Sequence Hub User IDs of your collaborators and make sure that **Has Access** to Sequence Hub - US (or EU, for the European Union instance) is selected. Then select **Grant access**\ ![](/files/Or6CEnoJTXBHh9zf86Gl) 6. Enterprise domain users only: There are two options to invite users either via a collaborative Enterprise domain account or via public Illumina account * After configuring new users, go to the **Users** tab via [Admin Console](https://help.connected.illumina.com/account-management/admin-console) to have access to a list of all the users invited and their respective permissions to different applications in a workgroup. "Has Access" will appear for applications the user can access, while a dash will indicate applications the user does not have access to. ![](/files/ocDTXSiOhudQpqo4zo6B) Users can be selected to open a detailed view showing which workgroup the user is part of and the applications those workgroups have access to. ![](/files/ltkNGmnF90rkh020EUwl) To change permissions, select the **"Change Access"** option in the top right corner. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #2874), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000002874%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to make sure Universal Copy Service is configured to Log On as a standard (non admin) account Universal Copy Service (UCS) is used to copy raw run files to the correct locations. To do this in a secure manner, it is important that UCS is running with standard user permissions. The instructions provided below show how to confirm that the settings are correct on Windows instruments. **For NovaSeq 6000** On the NovaSeq 6000, the **Illumina Universal Copy Service** runs as a process and uses the currently logged in account. To perform sequencing, always login with a standard (non-administrator) account. To verify you are sequencing using a standard account: * Login to the instrument using the account you plan to perform sequencing with * Follow the guide [How to check if a Windows account is a standard or administrator account](/instrumentation/general/instrumentation-general-reference_material-list/000007826) **For Benchtop Windows 10 Instruments** **Note**: The instructions for confirming and changing UCS log on credentials will vary based on the Local Run Manager version installed, see below for guidance on each version. ***To check the LRM version currently installed:*** Open the Local Run manager application and the version should be displayed at the bottom of the page: ![](/files/k0HQq3evABNqo2wt4P3c) ***For instruments running Local Run Manager v4.x:*** Services credentials should be updated directly from Local Run Manager, via the *System Settings* menu: 1. Log in to LRM using an admin account; 2. Go to the "**Tools**" menu on the top of the screen and select "**System Settings**" (Figure 1); 3. From the "System Settings" menu, go to the "SERVICE ACCOUNTS" tab and select "**Windows Account**" for "Universal Copy Service" and enter the Windows account credentials with user privileges (sbsuser for example) and click "Save" (Figure 2): ![](/files/bGT6eAz1Uiwdx8ULEYL1) **Figure 1.** Navigating to System Settings within Local Run Manager menus. ![](/files/wzNuYFIkeIDlZtQxeNNO) **Figure 2.** Setting Universal Copy Service to use the sbsuser log on credentials. ***For instruments running Local Run Manager v3.x:*** ![](/files/uDEBtnxQ7TkZDprSrKVJ) Follow the steps below to ensure that **Illumina Universal Copy Service** Windows service is configured to **Log On As** a standard or administrator Windows account. 1. Log into Windows using the **sbsadmin** (or other administrator) account. 2. Open the Windows **Services** app. * Select the **Windows Icon** in the lower left. * Begin typing "Services" and the **Services Desktop App** will appear in the results. * Select **Open** (Figure 3). ![](/files/pXgxsCH9uaJ338MDViAk) **Figure 3.** Opening Services app from the Windows Search bar. 3. Locate the **Illumina Universal Copy Service** within the list of services. Make note of the account name in the **Log On As** tab (.\*\*MyUser\*\* in this example) (Figure 4). ![](/files/2t1j8DA3VXr4UWDP8OCm) **Figure 4.** Illumina Universal Copy Service with the .\MyUser under the Log On As column 4. For the UCS account identified above, perform the corresponding action below to ensure UCS is configured to **Log On As** a standard account: 1. **Local Service** * No action required. 2. **Local System** (factory default) * Change UCS service to Log On As the Local Service account 3. **.\sbsadmin** * Change UCS service to Log On As a new or existing standard account (i.e. sbsuser) ***AND*** [Cache network storage credentials within standard account](/instrumentation/general/instrumentation-general-reference_material-list/000007828) 4. **.\sbsuser** * [Check if .\sbsuser is a standard user](/instrumentation/general/instrumentation-general-reference_material-list/000007826) * ***IF***standard: No action required. * ***IF*** administrator: [Downgrade .\sbsuser from an administrator to a standard account](/instrumentation/general/instrumentation-general-reference_material-list/000007827) 5. **All Other accounts** (On or Off-domain) * [Check if Log On As account is a standard account](/instrumentation/general/instrumentation-general-reference_material-list/000007826) * ***IF*** standard: No action required. * ***IF*** administrator: * [Downgrade Log On As account from an administrator to a standard account](/instrumentation/general/instrumentation-general-reference_material-list/000007827) (may impact some LRM Modules) ***OR...*** * Change UCS service to Log On As a new or existing standard account ***AND*** [Cache network storage credentials within standard account](/instrumentation/general/instrumentation-general-reference_material-list/000007828) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7852), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007828%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to recover passwords for Control Software accounts on the MiSeq i100 and NovaSeq X Series Instruments **Background** All Control Software User accounts on the MiSeq i100 and NovaSeq X Series platforms require a password to login, which needs to be updated at regular intervals. Sequencer Operator accounts can update their password when prompted by a password expiration notification. Administrator accounts can reset Sequencer Operator and Administrator account passwords at any time. When an Administrator resets a password for another User account, a temporary password is set, and the User can sign in using this temporary password to then set their new password. **Resetting a Control Software User password** 1. Initialize the MiSeq i100 or NovaSeq X Series Control Software and log in to an Administrator account. 2. Access the Users user interface (UI): 1. NovaSeq X Series: 1. Select the **instrument icon** to open the global navigation menu. 2. Select **Settings**, and then select **Users**. 2. MiSeq i100 Series 1. Select the **menu icon** in the top-left corner. 2. Select **Settings**, and then select **Users**. 3. Select the **User** to edit. 4. Select **Reset password** and input a new temporary password for the User account. 5. Select **Save**. 6. Log out of theAdministrator account and then login to the User account using the temporary password. 7. Input a **new password** for the User account, then re-enter the password to confirm. For additional information, see the platform-specific Product Documentation: [System Configuration - User Accounts](https://support-docs.illumina.com/IN/NovaSeqX/Content/UserRequirements.htm) section of the NovaSeq X Series Product Documentation. [Settings - People - Users](https://support-docs.illumina.com/IN/MiSeqi100Series/Content/IN/MiSeqi100/SysAccounts.htm) section of the MiSeq i100 Series Product Documentation. **Using the "Forgot Password?" Recovery Option** If the user Security Questions have been configured, users can select the **Forgot Password?** option to recover the password. See Knowledge Base Article [Configuring User Security Questions on the MiSeq i100 and NovaSeq X Series Platforms](/instrumentation/general/instrumentation-general-reference_material-list/000010191) for details. 1. On the Control Software local login screen, select **Forgot Password?** to initiate password recovery (Figure 1). 2. Answer the **Security Questions** configured for that User account, then select **Continue** (Figure 2). 3. After verifying the User identity, input a new password and re-enter the password to confirm, then select **Reset** (Figure 3). 1. The Password Recovery process resets the password and does not use a temporary intermediate password. 4. On the local login UI, login to the User account using the **new password**. ![](/files/Ri5rv1BLagYUpxt6LcaC) **Figure 1**: The Forgot Password? selection on the local login screen. ![](/files/CrN8OnuzGMVs1lleU9gD) **Figure 2**: Answering the Security Questions to authenticate the user. ![](/files/0AaHvIePxDqBAxHvaD4l) **Figure 3**: Resetting the User password after correctly inputting the Security Questions. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7773), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000010191%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to requeue a NextSeq 1000/2000 run locally (on the instrument) An analysis can be requeued locally from the Process Management screen in the NextSeq 1000/2000 Control Software. **Requirements to requeue an analysis:** 1. The System is NOT currently sequencing. 2. The original run folder has not been deleted from the instrument. 1. The run cannot be requeued once it has been deleted from Disk Management. 3. The run is listed as successfully completed in the control software. **Follow the steps below to requeue local analysis:** 1. Select the menu in the top left corner > Process Management\ ![](/files/sGrxMjvaC6ZckE9Z8czN) 2. Identify the run to be requeued ![](/files/aLkv5DHhLxnjdNZ23nOq) 3. Under the "Sample Sheet" select "Choose..." and navigate to desired Sample Sheet. ![](/files/5hmrU77xoJZABHz9TK7r) When requeuing analysis: * A new v2 sample sheet can be used. Transfer the sample sheet on a USB drive or network drive accessible to the instrument, and browse to it. * A new output directory can be selected. If outputting to an external hard drive results in an error, the only local location that is large enough to be used as an output folder is /usr/local/Illumina/Images. * If a new output directory is not selected, the new output data will be written to a new subfolder in the original output directory. Example: OutputDirectory/2/Data \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5816), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005816%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to requeue and import run data for reanalysis with Local Run Manager The Local Run Manager software is an integrated solution for recording samples for a run, specifying run parameters, monitoring run status, performing data analysis, and viewing results. This article describes how to requeue analysis for a run in Local Run Manager with the same module, and how to import data to analyze with a new module. **To requeue with the same module:** 1. From the Local Run Manager dashboard, select **Actions** next to the run you wish to requeue. Select **Requeue**. ![](/files/sJgbEhNLBGyO6KhlCsEc) 2. In the pop-up window, choose whether to **Edit Setup** or to **Requeue** with the original setup information. ![](/files/IoVN94SP7Im2aglb1AbH) * If **Edit Setup** was chosen, change the desired parameters, then select **Requeue Analysis**. The status shows “Analysis Completed” when the requeued analysis has completed **To import data to a new analysis module:** Importing run data can be used to reanalyze an existing run in a new workflow, or for off-instrument analysis. 1. From the dashboard, select **Create Run** and the desired module. On the next page, set the run parameters, then select **Save Run**. The run parameters must be the same as the original run. Important information to include is the read type and number of read cycles, the number and length of index reads, and whether custom primers were used. The original run setup can be determined in different ways depending on the source data: 1. For runs previously analyzed in Local Run Manager, select the original run in the Dashboard. Select the **Samples & Results** tab then **Requeue Analysis**. Select **Edit Setup** to view the run configuration. 2. When using Local Run Manager, the **Import Sample Sheet** option can be used to autopopulate the read and sample information. 3. The number of read cycles for a run can be found in the RunInfo.xml file in the run folder. 4. For more information on setting module-specific parameters, refer to the [analysis module workflow guides](https://support.illumina.com/sequencing/sequencing_software/local-run-manager/documentation.html).\ ![](/files/EBR5aYvDNFkTLrPabFYB) 2. In the dashboard, identify the run that was just created. 3. Select More Options (three vertical dots) next to the newly created run, and select **Import**. ![](/files/p97VTqDo8IkYu7ivAQjt) 4. Enter the full run folder path and the output folder location.**Note:** Local Run Manager does not support mapped drives or directories, but does support Universal Naming Convention (UNC) paths. Local Run Manager may fail to import runs from locations under user-specific folders, such as Desktop and Documents. Importing runs from universally accessible locations is recommended. Runs imported from network locations may take longer to analyze than runs imported from a local drive.\ ![](/files/q32iWRqVErYzRVXiI9Tz) 5. Select **Import Run** to start the analysis. The status shows “Analysis Completed” when the requeued analysis has finished. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1324), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001324%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to restart a sequencer after a power outage In the event of a power outage, an Uninterruptable Power Supply (UPS) sustains power to the instrument for a brief period of time. If the UPS fully discharges, or no UPS is connected, the sequencer will lose power, and if there is a run in progress, the run will be aborted. When the power is restored, follow guidance in the instrument's system guide to power the system back on. * If the instrument was idle at the time power was lost, no additional actions are needed, provided that the control software initializes successfully. * If a run was in progress when power was lost, the run terminates, the data and reagents cannot be recovered, and the run cannot be resumed. After powering up the sequencer, perform a manual post-run wash before the next sequencing run. This step is not required for the iSeq 100, NextSeq 1000/2000, or MiSeq i100 Series, as these are dry systems. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #6975), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000006975%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to set up a PhiX validation run with Local Run Manager A PhiX validation run confirms proper hardware and software performance of the instrument. The Illumina PhiX control library is a well-balanced genome with relatively equal representation of A, C, G and T nucleotides. Standard PhiX lacks indexes and is not an appropriate tool for assessing index read performance. PhiX validation runs can be set up on instruments with the Local Run Manager software suite bundled for on-instrument use. These instruments are the iSeq 100; MiSeq with MiSeq Control Software v3 and v4; NextSeq 500/550 with Control Software v4; and MiniSeq. Please note that while different control software versions will be running slightly different versions of the Local Run Manager, the run setup process for a PhiX run is the same. 1. Launch the Chromium browser and enter in the address bar. If required, enter the user ID and password. ![](/files/LZuIkzfQtoHfEv7GZaRO) 2. Select **Create Run** and choose **Generate FastQ** from the drop-down list. ![](/files/a4cynIpo05GrGAmpOrVI) 3. Enter the following values in the highlighted fields: * ``` * **Run Name**: PhiX validation run ``` ``` * **Library Prep Kit**: Custom * **Index Reads**: 0 (**Note:** PhiX is unindexed and selecting 1 or 2 Index reads can cause the run to terminate prematurely) * **Read Type:** Paired End * **Read Length:** Enter at least 26 cycles for each read (or follow Illumina Support guidance on the number of cycles for each read) ![](/files/j9ZT6D7RRjSsxy8c7l5U) ``` 4\. Keep default values in the **Module-Specific Settings** field. 5\. Scroll to the bottom of the Create Run page. In the Import Samples table, type PhiX in the **Sample ID** field. 6\. Select **Save Run**. ![](/files/KI1pHD0HPPDw9QVrqq4i) 7. Close the browser window and return to the instrument Control Software. 8. Select the **Local Run Manager** run setup option and then select ‘**PhiX validation run**’ from the list of available runs and proceed to sequencing. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1318), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001318%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to switch Operating System user accounts on Illumina Windows 10 Sequencing Systems **Background** Illumina sequencing systems (iSeq 100, MiniSeq, MiSeq RUO and NextSeq 500/550) that are running the Windows 10 operating system are installed with both standard and administrator level accounts. These are typically **SbsAdmin**, an administrator level account and **SbsUser**, a standard level account. **Note**: Some earlier installed NovaSeq 6000 systems have a version of the Windows 10 image that have only the SbsUser account with administrative privileges. Later systems with a newer Windows 10 image have both SbsAdmin and SbsUser accounts with privileges like the above desktop systems. The **SbsAdmin** user account is not typically used for sequencing runs but rather for various system management operations that require administrative privileges (e.g., updating the control software, configuring network settings, and troubleshooting the system by Illumina staff). **SbsUser** is typically used for standard operation of the system and conducting sequencing runs. In order for the user to perform control software updates and other administrative tasks, it is required to switch to the **SbsAdmin** account. **Note**: Switching OS accounts must only be done while the system is idle. Doing so while the system is performing a sequencing run risks premature termination. **How to switch the OS user account:** 1. On the Windows desktop, Click the **Start** button in the lower left corner of the screen. 2. Select the **username** icon or picture. 3. Select **switch user** or **log out.** 4. Once logged out or on the switch user screen, Log into the **SbsAdmin** Windows administrator account. **Note**: Repeat this procedure to log back into the **SbsUser** account before performing the next sequencing run. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7855), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007855%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to thaw and store sequencing reagents for optimal performance Sequencing reagent performance depends on thawing technique and thawed reagent storage time and conditions. It is important to understand and follow the validated recommendations for reagent thawing and storage as some reagents contain enzymes that are sensitive to time stored at different temperatures. Unless specified below, refreezing thawed reagents can negatively affect enzyme activity and run performance. **iSeq 100 Reagent Kits (**[**Reagent stability and thawing for the iSeq 100**](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Reagent-Stability-and-Thawing-for-the-iSeq/README.md)**)** * After receiving reagent shipment, store reagent cartridge in the freezer at -20°C to -25°C with the arrow pointing up for at least 24 hours before thawing for use. * There are several ways to thaw the reagent cartridge: * Thaw in a room temperature water bath (20°C to 25°C) for a minimum of 6 hours, the cartridge is stable up to 18 hours in the water bath.\ \- It is important to store the reagent cartridge at -20°C for at least one day before use. If the reagent cartridge is moved directly from dry ice shipment to a water bath thaw, this can heat shock the fluidics systems and cause total run failure. * Thaw in a refrigerator (2°C to 8°C) for a minimum of 36 hours, not exceeding 1 week. * Thaw at room temperature air (20°C to 25°C) for a minimum of 9 hours, the cartridge is stable up to 18 hours in room temperature air. * Reagents must be used immediately after thawing (within the recommended time ranges described above), and re-freezing reagents is not recommended or supported. The longest thaw time stability is 1 week at 4°C. **MiSeq v2 and v3 Reagent Kits (**[**Reagent Stability and Thawing Guidelines for MiSeq Sequencing Kits**](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Instrumentation-MiSeq-Reagent-Stability-and-Thawing/README.md)**)** * After receiving reagent shipment, store reagent cartridge in the freezer at -20°C. * There are several ways to thaw the reagent cartridge: * **v2 cartridges**: Thaw in a room temperature deionized water bath with enough water to submerge the base of the reagent cartridge for 60 minutes. Place on ice or set aside at 2°C to 8°C and use within 6 hours. * **v3 cartridges:** Thaw in a room temperature deionized water bath with enough water to submerge the base of the reagent cartridge for 60-90 minutes. Place on ice or set aside at 2°C to 8°C and use within 6 hours. * **v2 and v3 cartridges:** thawed overnight at 2°C to 8°C, store at 2°C to 8°C for up to 1 week. * Thawing the reagent cartridge overnight in the refrigerator allows for more flexibility as the reagents are then able to be stored at 4°C for up to one week. ### **MiniSeq Reagent Kits (**[**Thawing and Stability Guidelines for MiniSeq Reagent Kits**](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Thawing-and-Stability-Guidelines-for-MiniSeq-Reagent-Kits/README.md)**)** * After receiving reagent shipment, store reagent cartridge in the freezer at -20°C. * There are several ways to thaw the reagent cartridge: * Thaw in a 37°C water bath for 35 minutes, it is stable up to 2 hours. * Thaw in a room temperature water bath (19°C to 25°C) for 90 minutes, it is stable up to 24 hours. * Thaw at room temperature air (19°C to 25°C) for 5 hours, it is stable up to 24 hours. * Thaw at 2°C to 8°C for 18 hours, it is stable up to 72 hours. * If reagents need to be stored during troubleshooting, store them at 4°C until ready to run within the stability time frames listed above. * **NextSeq 500/550 Reagent Kits (**[**Instructions for thawing and storing NextSeq 500/550 reagents**](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Instrumentation-NextSeq-550-Reagents-and-Stability/README.md)**)** * After receiving reagent shipment, store reagent cartridge in the freezer at -20°C. * There are several ways to thaw the reagent cartridge: * Thaw in a room temperature deionized water bath for 60 minutes, place on ice or set aside at 2°C to 8°C, and use as quickly as possible or within the same day. * Thaw overnight at 2°C to 8°C, store at 2°C to 8°C for up to 1 week.\ \- Note: Reagents require a minimum of 18 hours to thaw. **NextSeq 1000/2000 Reagent Kits (**[**Thawing and reagent preparation guidelines for the NextSeq 1000/2000 reagents**](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Thawing-Guidelines-for-the-NextSeq-2000/README.md)**)** * After receiving reagent shipment, store reagent cartridge in the freezer at -20°C with the arrows pointing up, in their original box, to avoid tearing or puncturing the foil bag. * There are several ways to thaw the reagent cartridge: * *XLEAP-SBS Sequencing Kits*\ \- Water Bath: Thaw in temperature controlled 25°C water bath with a minimum of 9.5 cm water depth for 8 hours. Do not exceed 10 hours.\ \- Refrigerator (2°C to 8°C): One day prior to anticipated run, remove cartridge from -25°C to -15°C storage. Thaw at room temperature for 6 hours. Transfer to refrigerator at 2°C to 8°C, then continue to thaw for a minimum of 16 hours. The cartridge is stable up to 72 hours in the refrigerator. During the room temperature thawing time, cartridges must have air on all sides except the bottom and must not be stacked. In the refrigerator, cartridges may be stacked but must be given space on all other sides.\ \- Room temperature (20°C to 25°C): Place cartridges on wire rack for 12 hours and do not exceed 16 hours. During the room temperature thawing, cartridges must have air on all sides and must not be stacked. * *Standard SBS Sequencing Kits*\ \- Water bath: Thaw in temperature controlled 25°C water bath, with a minimum of 9.5 cm water depth for 6-8 hours for 300 cycle or smaller kits; and 600 cycle kits require 8-10 hours.\ \- Refrigerator (2°C to 8°C): One day prior to anticipated run, remove cartridge from -25°C to -15°C storage. Thaw at room temperature for 6 hours. Transfer to refrigerator 2°C to 8°C, and continue to thaw for a minimum of 12 hours for 300 cycle or smaller kits; or continue to thaw for a minimum of 16 hours for 600 cycle kits. The cartridge is stable up to 72 hours in the refrigerator. When thawing at room temperature, cartridges must have air on all sides except the bottom and must not be stacked. In the refrigerator, cartridges may be stacked but must be given space on all other sides.\ \- Room temperature (20°C to 25°C): Place cartridges on wire rack for a minimum of 9-16 hours for 300 cycle or smaller kits; 12 hours (16 hour maximum) for 600 cycle kit. * If using the refrigerator thaw method or removing it from fridge storage, remove the thawed cartridge from 2-8ºC storage. Set the unopened cartridge aside at room temperature for at least 15 minutes before sequencing. Do not exceed 1 hour. * If using room temperature thaw, proceed to Load Consumables Step. **NovaSeq 6000 Reagent Series (**[**Thawing, stability, and storage of NovaSeq 6000 reagents**](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Thawing-Stability-and-Storage-of-NovaSeq-6000-reagents/README.md)**)** * After receiving reagent shipment, store Cluster and SBS cartridges in the freezer at -20°C. * Thaw the Cluster and SBS cartridges in a room temperature deionized water bath: * *NovaSeq Cluster and SBS cartridges*\ \- Thaw SP, S1, and S2 Cluster cartridges in a room temperature deionized water bath for 2 hours.\ \- Thaw S4 Cluster cartridges in a room temperature water bath for 4 hours.\ \- Thaw SP, S1, S2, and S4 SBS cartridges in a room temperature water bath for 4 hours. * *NovaSeq XP Workflow Reagents*\ \- Thaw DPX1, DPX2 and DPX3 at room temperature for 10 minutes, then set aside on ice.\ \- For best results, use as soon as possible. For the best performance, prepare the ExAmp master mix immediately before use. Store the ExAmp master mix up to 1 hour on ice, or 30 minutes at room temperature. After loading the libraries and ExAmp, load flow cells onto the instrument within 30 minutes. If ExAmp reagents cannot be used, they can be refrozen one time only. If refreezing, do so immediately after thawing. * Store thawed reagents (Cluster and SBS cartridges) at 2°C to 8°C until use for up to 24 hours. Cluster and SBS cartridges can be refrozen once at -20°C if run cannot be started right away. * SBS cartridges are sensitive to light. **NovaSeq X Series (**[**Reagent stability and thawing guidelines for the NovaSeq X Series**](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Reagent-Stability-and-Thawing-Guidelines-for-NovaSeq-X-NovaSeq-X-Plus-Platform/README.md)**)** * All kit components are shipped at ambient temperature, and have been qualified to remain at ambient temperature for up to 10 days during shipment. When the reagents are received, promptly store components at the indicated temperature for proper performance. *Reagent Cartridge* * There are two validated methods for thawing a NovaSeq X Series reagent cartridge: * Water Bath: Remove cartridge from box, then remove cartridge from the bag. Submerge reagent cartridge in laboratory-grade water bath at 15°C to 30°C until the water reaches the bottom of the cartridge cover. Thaw for 4 hours and do not exceed 24 hours. Load cartridge into instrument within 24 hours. If reagents cannot be used within 24 hours, store at 2°C to 8°C for up to 72 hours or return to -25°C to -15°C storage for up to 7 days. After thawing, do not refreeze more than one time.\ \- \[25B, 10B, 5B] To confirm reagents are thawed, inspect the position #30 well on the underside of the cartridge and make sure that the contents are free of ice. For the NovaSeq X Series 1.5B Reagent Kit, Illumina recommends strictly following the provided thaw conditions and times. Visual checks to confirm reagents are thawed might not be accurate for this kit. * Refrigerator: Remove cartridge from box, then remove cartridge from the bag. Thaw in a 2°C to 8°C refrigerator for 48 hours. If reagent cartridge cannot be loaded into the instrument within 24 hours, store at 2°C to 8°C for up to 72 hours or return to -25°C to -15°C storage for up to 7 days. After thawing, do not refreeze more than one time. * Invert the cartridge 10 times to mix reagents. * Gently tap the bottom of the cartridge on the bench to reduce air bubbles. *Lyo Insert* * Remove from -25°C to -15°C storage and thaw at room temperature for 10 minutes. * If Lyo Insert cannot be used within 24 hours, return to -25°C to -15°C storage. After thawing, do not refreeze more than one time. *Pre-load and Custom Primer Buffers* * Remove from -25°C to -15°C storage and thaw at room temperature for 10 minutes. * Invert 5 times. * If buffers cannot be used within 8 hours, return to -25°C to -15°C storage. After thawing, do not refreeze more than one time. **MiSeq i100 (**[**Reagent Stability Guidelines for the MiSeq i100 Series Consumables**](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Reagent-Stability-Guidelines-for-the-MiSeq-i100-Series-Consumables/README.md)**)** * All kit components are shipped and stored at room temperature, so there are no thawing steps required when preparing a sequencing run. However, once the packaging has been opened, the reagent kit and associated consumables should be used within the time specified below for optimal performance. *Dry Cartridge* * Keep dry cartridge in the foil packaging until it is ready to be loaded. The Dry Cartridge must be used within 4 hours of opening the foil packaging. *Wet Cartridge* * Keep wet cartridge in the foil packaging until it is ready to be loaded. The Wet Cartridge must be used within 4 hours of opening the foil packaging. *Denatured Libraries (Libraries + KLD Buffer)* * Store the denatured libraries on ice after mixing the diluted libraries with the KLD buffer. The denatured libraries are stable on ice or at 4° C for up to 6 hours. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1533), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009351%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to update Network Credentials in Windows Credential Manager on Windows 10 Platforms **Background** Windows Credential Manager is a built-in tool within Windows 10 that is used to store network credentials used when authenticating connections to network storage. Adding network credentials to Credential Manager is a critical step for ensuring that Local Run Manger and Universal Copy Service have appropriate access to network storage. If the network credentials change, see the following steps to update them within Credential Manager and restore network storage access. **Resolution Actions** 1. Ensure that the user is logged in as the account that is used for sequencing, typically **sbsuser**. 2. In the Windows Search bar, input **Credential Manager** and then select the **Credential Manager** application (Figure 1). 3. Select **Windows Credentials** (Figure 2). 4. Under the **Windows Credentials** header, locate the mapped network storage connection, then click the **down arrow** to expand the selection (Figure 3). 5. Select **Edit** (Figure 3). 6. In the User name and Password text boxes, input the updated network credentials as necessary (Figure 4). 7. Select **Save**. 8. **Close** the Windows Credential Manager application. 9. **Power cycle** the instrument to refresh the mapped network connection. ![](/files/NjYxU5GXACl90FWy2oT4) **Figure 1**: Credential Manager application in the Windows Search menu. ![](/files/uVNpAmq3a8sVqFBibrdT) **Figure 2**: Windows Credential tab with the Windows Credentials header showing the mapped network drive. ![](/files/Qm5eOzLxCH8xp32JtDQc) **Figure 3**: The down arrow used to expand the selection and the Edit button to update the credentials. ![](/files/xTyvH7AhL8rRQkQomUBX) **Figure 4**: The Edit Windows credential user interface (UI) showing the User name and Password text boxes. \ \ \
| | | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #10020), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000010020%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # How to update Windows 10 account credentials on Benchtop Instruments Benchtop Instruments running the Windows 10 Operating System (OS), may require periodic password updates. When prompted, as shown in **Figure 1a**, select OK, then update the Windows password, as shown in **Figure 1b**. ![](/files/CJjcBK9ZNdkUKPAI5jME) **Figure 1a.** Password update prompt. ![](/files/8NrAx2tuXcu9d03M5Xql) **Figure 1b.** Password update. **Actions Post Password Update:** Universal Copy Service (UCS) and Local Run Manager (LRM) are components of the Control Software which are used to transfer sequencing run data, setup runs, and analyze data. These components run as Windows services which may be configured to **Log On As** any Windows account. Changing the password of a Windows account running UCS or LRM services does not automatically update the passwords for the services. See below for instructions to update the UCS and LRM service passwords following a Windows account password update. If the password for a Windows account which is running the UCS and LRM services is updated in Windows, but not in the LRM and UCS services, the instrument may fail to operate. Disabled operation prevents new run settings from being entered and data transfer from completing. Control software may fail to initialize, or the following errors may occur. **Error message:** * "Cannot initiate communication with Universal Copy Service. Make sure that the service is installed and started." * "The following required software is either not installed or not running. Sequencing cannot be performed until this problem is fixed. Contact Illumina Technical Support. Universal Copy Service." **To update UCS and LRM service credentials with Local Run Manager v3.x or below, see the following instructions:** 1. Select the Windows icon in the lower left corner of the screen. In the Windows search field, enter **Services**. When **Services** appears in the results, right-click and select **Run as administrator**. 1. ![](/files/U0zWRJt9mRYFnx597qSc) 2. If prompted, enter administrator credentials (by default the credentials will be the **sbsadmin** user credentials) in the pop-up window. 3. Locate the Illumina services. 4. Right-click on **Illumina** **Local Run Manager Analysis Service**. Select **Stop**. 1. ![](/files/hOnGq28mG5Woikne8JSN) 5. Right-click again on **Illumina Local Run Manager Analysis Service**. 6. Select **Properties** and navigate to the **Log On** tab. 7. Select **This account** and **Browse**... to search for the account. In the **Select User** window, select **Advanced** and then **Find Now**. Select the Windows account for which the password was just updated (default **sbsuser**) from the search results. 1. ![](/files/KJvNRcpczadue7gT3rZV) 8. Select **OK** to acknowledge both windows. 9. Enter the new account (default **sbsuser**) password, select **Apply** and **OK**. 10. Restart the service. 11. Repeat steps 4-10 for **Illumina Local Run Manager Job Service**, **Illumina Universal Copy Service**,and **Illumina Run Copy Service** if they are present in the list. 12. Shut down and restart the system. **To update UCS and LRM service credentials with Local Run Manager v4.x, see the following instructions:** 1. In Local Run Manager (LRM), configure the Illumina services to use respective **Log On As** accounts via the admin account by accessing the **Tools** menu. 1. ![](/files/D4jRExHsjyW4JZnvRqkZ) 2. Open **System Settings**, select **Service Accounts** and select the respective option for each **Service** (note that Illumina recommends Universal Copy Service is **ALWAYS** configured with the sbsuser account. 1\. ``` ![](/files/zw7VbykhxIlvCkr5U5Oj) ``` **Note:** If runs are saved **locally**, the Analysis Service and Job service should be set to Local System account and Universal Copy Service can be set to Local Service Account. [Contact Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support) for further assistance. **Additional Resources:** For more detailed instructions, first-time setup, or to update the Internet Information Services (IIS) LRM user credentials for importing runs, refer to the Knowledge articles [How to cache credentials for access to Network Storage and verify Read/Write access](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/How-to-cache-credentials-for-access-to-Network-Storage-and-verify-Read-Write-access-12/README.md) and [How to connect benchtop instruments and Local Run Manager to a network location.](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/How-to-connect-benchtop-instruments-and-Local-Run-Manager-to-a-network-location?r=1137\&ui-knowledge-components-aura-actions.KnowledgeArticleVersionCreateDraftFromOnlineAction.createDraftFromOnlineArticle=1) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1932), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001934%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # IT Requirements for Implementing Illumina Proactive Video In this video, we discuss IT requirements for implementing Illumina Proactive, an instrument performance monitoring service provided by Illumina that can increase instrument uptime, improve operational efficiency, and reduce the risk of lost resources. Learn more about Illumina Proactive [here](https://www.illumina.com/services/instrument-services-training/product-support-services/instrument-monitoring.html). < {% embed url="" %} Video length: 4:07 min \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #5749), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000005749%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Illumina 测序平台的最大读长 \
Illumina平台和测序试剂盒支持多种 [测序应用](https://emea.illumina.com/science/technology/next-generation-sequencing/plan-experiments/read-length.html) 。 为了保证最高水平的测序质量，Illumina不同测序平台以及不同的SBS试剂盒版本支持的最大读长有所不同，相关信息请参阅 [我所购买的SBS试剂盒最多能够满足多少个循环的测序？](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000007400) 技术文档。利用本地运行管理软件（ [Local Run Manager，LRM](https://support.illumina.com/sequencing/sequencing_software/local-run-manager.html)）或仪器控制软件（Control Software）设置测序运行时，可以选择更长的读长。但是当read长度超过支持的长度时，Illumina将无法保证较高的数据质量。 \ **表 1.** 测序平台和SBS试剂盒支持的最大读长 ![](/files/yzn8rB4c6iYFpMt5sQSE) \* MO: 中通量 / HO: 高通量 \ **Index Reads的最大读长**\ * 仪器控制软件：如表2所示，可在某些仪器的运行设置期间输入自定义Index读长： * LRM v2：Index读长最多可以设置100个字符（请参阅：[Local run Manager 2: 如何使用自定义文库制备试剂盒](https://emea.support.illumina.com/bulletins/2018/04/local-run-manager-2--how-to-use-a-custom-library-prep-kit.html)技术文档）。 * LRM v3：最多输入20个字符。如果需要20-100 bp读长，请选择手动上机模式。 * LRM v4：最多输入20个字符。如果需要20-1000 bp读长，请选择手动上机模式。 * 为确保Index Reads的测序质量，请勿超过Index支持的最大长度。 \ **表 2.** 测序平台的最大单个Index长度 ![](/files/zRxgq5XaA4hacRrBWwlV) \*通过云端设置测序运行时，Index长度会受到以下列出的 BCL Convert 限制。\ \*\*Index长度为20-1000bp之间时，通过手动模式设置测序运行，因为LRM V4的上限为20bp。\ \*\*\*手动设置测序运行不在测序仪进行分析的话，Index长度不受软件限制。 **请注意**，BCL Convert对Index长度是有限制的。BCL Convert 4.2以及之前版本，Index总长度不能超过27bp。 BCL Convert 4.3以及之后版本，Index长度限制提高到每个Index最长27bp。 如果使用 BCL Convert 设置override cycle，那么在Index读取中指定的用于 UMIs（U）的碱基将不会计入Index长度的计算中。 \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7102), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007102%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Illumina测序平台上每个测序步骤的运行时间预测 Illumina测序的运行时间包括簇生成、边合成边测序化学循环、双端化学反应和清洗步骤。此外，使用非Pattern模式的flow cell的运行在构建模板时会暂停一段时间。为了帮助规划测序工作流程和预测整体运行时间，表1根据Illumina测序平台和试剂版本总结了每个测序步骤的预估时长。 | 仪器 | 测序仪器上簇生成 | 每个循环的时间(分钟) | 模板构建暂停时间\* | 双端测序反转时间 | 运行后清洗/维护清洗 | | --------------------------- | ---------------------------------------------------------------------- | -------------------------------------------------- | ---------- | ---------------------------------------------- | ------------------------------------------------------------------------ | | iSeq 100 | 5小时 | 2.2 | N/A | 52 分钟 | 无需清洗 | | MiniSeq | 90分钟 | 3.5 | 运行继续 | 60 分钟 | 75分钟 | |

MiniSeq

(快速运行)

|

整体运行时间：

单index, 1x 101 -5.1小时

双index, 1x 101 -5.7小时

| N/A | 运行继续 | N/A | N/A | | MiSeq v2 | 60分钟 |

Nano = 2.5

Micro = 3

Full = 4.5

| 运行继续 | 31 分钟 | 运行后清洗20分钟，模板管路清洗30分钟，维护清洗90分钟 | | MiSeq v3 | 70分钟 | 6 | 运行继续 | 50 分钟 | 运行后清洗20分钟，模板管路清洗30分钟，维护清洗90分钟 | | MiSeq i100系列 | \~ 120分钟 | \~ 1分钟 | N/A | \~ 60 分钟 | N/A | | NextSeq 500/550 (中通和高通试剂) | 2.5小时 | 4.6 | 运行继续 | 60 分钟 | 90分钟 | | NextSeq 1000/2000 P1-标准 | 3.75小时 | 2.5 | N/A | 40 分钟 |

可选择性清除试剂：

1.5小时\*\*

| | NextSeq 1000/2000 P2-标准 | 4小时 | 4.7 | N/A | 40 分钟 |

可选择性清除试剂：

1.5小时\*\*

| | NextSeq 1000/2000 P3-标准 | 4小时 | 8.4 | N/A | 45 分钟 |

可选择性清除试剂：

3小时\*\*

| | NextSeq 1000/2000 P1-XLEAP | 4小时 | 1.7 | N/A | 74 分钟 | 可选择性清除试剂：1.3-3.2小时\*\* | | NextSeq 1000/2000 P2- XLEAP | 4小时 | 3.4 | N/A | 74 分钟 |

可选择性清除试剂：

1-3.2小时\*\*

| | NextSeq 1000/2000 P3- XLEAP | 5小时 | 6.4 | N/A | 80 分钟 | 可选择性清除试剂：1.4-2.7小时\*\* | | NextSeq 1000/2000 P4- XLEAP | 5小时 | 7.4 | N/A | 80 分钟 | 可选择性清除试剂：1.4-2.7小时\*\* | | NovaSeq 6000 | 180分钟¤ |

SP/S1 = 3.5
S2 = 5
S4 = 6.75

| N/A | 48 分钟 |

运行后清洗=80 分钟

维护清洗=80分钟

| | NovaSeq X系列 |

1.5B = 5小时
10B = 4.8小时
25B = 5.8小时

|

1.5B = 2.2分钟
10B = 2.7分钟
25B = 6.1分钟

| N/A |

1.5B = 67分钟
10B = 48分钟
25B = 84分钟

|

运行后清洗=110 分钟(1.5B流动槽清洗耗时180 分钟)

维护清洗=180分钟(1.5B流动槽不可用于维护清洗)

| ``` 表1：每台测序仪和该仪器支持试剂的每个测序步骤的大致时间 * 模板构建时间会根据簇密度而变化 ¤ XP的工作流程大约是150分钟，因为省略了ExAmp的步骤 # 在这些运行中第2-5个循环可能需要大约25分钟/每个循环 ** 清除试剂的时间根据循环次数而变化 ``` ### 预计运行时间将取决于簇密度和可用的计算机资源。如果硬盘没有足够的空间进行数据处理，或者网络定位速度很慢，运行时间可能会延长。Illumina平台最大读数长度的总运行时间，以及其他测序运行规格，可以在 [Illumina Sequencing Platforms](https://www.illumina.com/systems/sequencing-platforms.html) 上找到。 \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7137), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007137%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Illumina测序平台测试Run中PhiX的上机浓度
PhiX测试Run是Illumina用来确认测序仪硬件和软件是否可以正常工作的实验方法。这里所用的PhiX参照文库基因组碱基的平衡性很好，A，T，C，G四种碱基的比例相对均一。Illumina 目前提供两种类型的PhiX产品可供用户选择。 **PhiX Control v3** , 该文库没有Index 不适用于Index 测序的性能评估。这种推荐用于验证运行(validations runs)。更多信息可以点击查看[PhiX Control v3文库是什么，它在Illumina下一代测序中起到什么作用？](https://knowledge.illumina.com/library-preparation/general/library-preparation-general-reference_material-list/000007130) **PhiX** **Indexed Control**. 这种 PhiX 不推荐用于验证运行(validations runs)。 更多信息可以点击查看[PhiX Indexed Control (1000 Cycle) Product Information](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000009867) \ 测试时, 确保PhiX参照文库的簇密度落在最佳范围内对测试结果的准确性非常重要。请参考下面表格了解不同测序平台PhiX的上机浓度和簇密度建议（这些推荐的参数是基于**PhiX control v3** ）：\ | 测序平台 | 最佳上机浓度 | 最佳原始簇密度 | | ---------------------------------------------------------------------- | ---------- | ----------------------- | | iSeq 100 | 100 pM | N/A\* | | MiniSeq | 1.4 pM | 170-220K clusters/mm2 | | MiSeq v2 reagents | 12.5 pM | 1000-1200K clusters/mm2 | | MiSeq v3 reagents | 20 pM | 1200-1400K clusters/mm2 | | NextSeq 500/550 High Output reagents | 1.8 pM | 170-220K clusters/mm2 | | NextSeq 500/550 Mid Output reagents | 1.5 pM | 170-220K clusters/mm2 | | NextSeq 1000/2000 (Onboard, Standard chemistry, XLEAP chemistry P1/P2) | 650 pM\*\* | N/A\* | | NextSeq 2000 (Onboard, XLEAP chemistry, P3/P4 and 600-cycle P1/P2) | 450 pM\*\* | N/A\* | | NovaSeq 6000 - Standard Workflow | 250 pM\*\* | N/A\* | | NovaSeq 6000 - XP Workflow | 100 pM\*\* | N/A\* | | NovaSeq X - 1.5B/10B | 140 pM\*\* | N/A\* | | NovaSeq X - 25B | 140 pM\*\* | N/A\* | | MiSeq i100 | 120 pM\*\* | N/A\* | \*Patterned flow cells上面都有固定量的纳米孔，所以不同的run显示的簇密度都是相同的。如需评估簇密度情况，推荐通过[绘制 %Occupied 与 %PF 关系图](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000007138)查看。 \*\*为最终的上机浓度 对于PhiX测试Run，测序读长和参数可以根据实验目的进行调整，但是请注意Read1和Read2必须至少是26个Cycles，这样仪器上的数据分析软件才能生成质量分数（Quality Scores）。 \ 有关为Illumina测序平台准备PhiX测试Run的更多信息，请参见以下文档: * [iSeq 100 Sequencing System Guide](https://support.illumina.com/downloads/iseq-100-system-guide.html) * [MiniSeq System Denature and Dilute Libraries Guide](http://support.illumina.com/downloads/miniseq-denature-dilute-libraries-guide.html) * [Denature and Dilute Protocol Generator](https://support.illumina.com/downloads/denature-and-dilute-protocol-generator.html) (for MiSeq, NextSeq 500/550, NextSeq 1000/2000, NovaSeq 6000, MiSeq i100 and NovaSeq X Plus instruments) * [MiSeq i100 Series Product Documentation](https://support.illumina.com/sequencing/sequencing_instruments/miseq-i100-plus/documentation.html) **备注**: 推荐对Phix 原管储存液进行Qubit 或qPCR定量后再稀释到需要的浓度使用。 \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7139), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007139%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Illumina测序系统废液中甲酰胺的终浓度是多少？ 该技术文档提供的信息，能够帮助您计算Illumina测序反应废液中甲酰胺的终浓度。 每个测序反应废液中甲酰胺的浓度会基于测序平台和测序长度而有所差异。您可以根据下表的说明，测量废液的总体积，并计算甲酰胺的终浓度。 ![](/files/pYpBqHa2rzFBMzAFvQhE) \*由于iSeq100试剂槽不能打开，因此它是以固体废弃物处理。 \*\*如果剩余甲酰胺没有排入废液中，基于不同测序长度甲酰胺的浓度范围为0.35-1.5% **NovaSeq X/X Plus** NovaSeq X/X Plus的废液中甲酰胺浓度取决于所执行的Reads和Index读取的次数。
有关NovaSeq X/X Plus废液的更多信息，请参见[Handling and Disposal Recommendations for Used Reagents on the NovaSeq X/X Plus](https://knowledge.illumina.com/instrumentation/novaseq-x-x-plus/instrumentation-novaseq-x-x-plus-faq-list/000008392). **MiSeq i100 / i100 Plus** 试剂卡盒不含甲酰胺，可以像PCR产品废弃物一样丢弃。 请穿戴合适的个人保护装备安全处理甲酰胺试剂。在不同地区，根据废液中甲酰胺和其它有害成分，对废液的处理也有所差异。请联系当地的环境卫生和安全（EH\&S）办公室，确定对有害物质的界定以及如何处理容器和未使用的有害物质，以符合环境安全。如果需要Illumina试剂中化学成分的更多信息，请参考Illumina支持页面中的[安全数据表（SDS）](https://support.illumina.com/sds.html)。 \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7131), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007131%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Illumina非Pattern Flow Cell测序平台簇密度推荐指南
簇密度是决定测序中能否获得最佳的测序质量和数据量的重要因素。下表是根据平衡文库（例如phix 文库）的结果，列出的各平台原始簇密度推荐值： | 测序平台 | 模式/试剂 | 原始簇密度理想值 | | --------------- | -------------------------- | -------------------------- | | MiSeq | v2 | 1000-1200 K/mm2 | | v3 | 1200-1400 K/mm2 | | | MiniSeq | Mid and High Output | 170-220 K/mm2 | | NextSeq 500/550 | Mid and High Output | 170-220 K/mm2 | 其中iSeq 100, MiSeq i100系列, NextSeq 1000/2000, NovaSeq 6000, NovaSeq X 系列测序平台使用的Flow Cell为Pattern Flow Cell, 这种类型的Flow Cell即使是上面所有纳米孔都没有成簇，簇密度也都为同一固定值。在使用这些平台时可以通过Cluster PF(%)对Cluster Occupancy做出初步的判断。 详情请参阅以下资料: * [通过绘制% Occupied和% Pass Filter散点图，优化NovaSeq 6000和iSeq 100测序平台的上样浓度](https://knowledge.illumina.com/instrumentation/general/instrumentation-general-reference_material-list/000007138) * [Calculating Percent Passing filter for Patterned and Nonpatterned Flow Cells](https://www.illumina.com/content/dam/illumina-marketing/documents/products/technotes/hiseq-x-percent-pf-technical-note-770-2014-043.pdf) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #7415), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000007415%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Impact of ammonium based cleaning products on sequencing run performance Illumina has recently discovered that use of ammonia-based cleaners or sanitizing products near sequencing run setup (lab benches, pipettes, etc.) can result in decreased sequencing run performance metrics. Decreased or variable cluster densities and low starting intensities have been seen by customers. The mechanism by which this effect occurs may be linked to the effect of ammonia on DNA structure ([Zinchenko et al 2004](https://www.ncbi.nlm.nih.gov/pubmed/14997528)). If you are experiencing variable cluster density (on nonpatterned flow cells), variable percent clusters passing filter (for both patterned and nonpatterned flow cells), or lower than expected starting intensities on your sequencing runs, make sure that ammonia-based cleaners are not used in the lab environment. Inspect ingredient lists of cleaners or antibacterial wipes for ammonia or quaternary ammonium compounds such as benzalkonium chloride (alkyldimethylbenzylammonium chloride) and dialkyldimethylammonium chloride. If ammonia-based cleaners have been used, Illumina recommends: * Extensively clean equipment and surfaces that have been in contact with the ammonia-based cleaners. To clean, use an anionic detergent such as 1% SDS or diluted dish soap, followed by water. * Use pipettes that have not been in contact with ammonia-based cleaners when setting up clustering and/or sequencing runs. **Additional Resources:** [Decontaminating Illumina instruments for novel coronavirus (2019-nCoV)](https://support.illumina.com/bulletins/2020/03/decontaminatingillumina-sequencing-instrumentsfor-novel-coronavi.html) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1846), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001846%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Index color balancing for XLEAP SBS reagents on the NextSeq 1000/2000 and NovaSeq X Series Selecting Index Adapters with diverse index sequences that optimize color balance within pooled libraries is crucial for successful demultiplexing and data analysis. As a general guideline, Illumina recommends selecting index sequences such that signal will be present in both channels for each index cycle when sequencing libraries on a 2-channel system. Like Illumina's other sequencers utilizing 2-color chemistry, the XLEAP-SBS reagents for the NextSeq 1000/2000 and NovaSeq X Series systems uses two fluorescent dyes and two images to encode data for the four base calls. However, the XLEAP-SBS chemistry has updated C to the dual-color base and A to the single, blue-channel only base. This differs from other two-color SBS chemistry where A is the dual-color base. For more information on this, see the Knowledge articles [Chemistry and Imaging on the NovaSeq X Series Instruments](https://github.com/illumina-swi/illumina-knowledge/tree/master/articles/Knowledge/Chemistry-and-Imaging-on-the-NovaSeq-X-X-Plus-Instruments/README.md) and [Chemistry and imaging on the NextSeq 1000/2000](/instrumentation/nextseq-1000-2000/instrumentation-nextseq-1000-2000-reference_material-list/000003035). ![](/files/F9BbI0bv9QkPkCB7UMko) **T** = Green\ **C** = Blue + Green\ **A** = Blue\ **G** = Dark (no label) Due to this change, indexing combinations need to be reviewed and potentially revised to make sure that signal is present in both channels for each index cycle during runs on XLEAP chemistry. When sequencing using XLEAP chemistry, combine index sequences so that signal is present in both channels for every cycle whenever possible. It is acceptable to have signal only in the green channel from the T or C bases, if needed. Illumina recommends avoiding index combinations which only have signal in the blue channel from A or A+G in any given cycle, or no signal (only G) present in any given cycle. For larger pools, it is recommended to maintain base and color balance for all pooled indexes in each lane. Testing is required to confirm index combinations not listed in [Index Adapters Pooling Guide](https://support.illumina.com/downloads/index-adapters-pooling-guide-1000000041074.html), and for third-party or custom index combinations to make sure the index selections work reliably. When sequencing on a two-channel system, either of the first two cycles of the Index Read must start with at least one base other than G. If an Index Read starts with two G bases, signal intensity is not generated and this can cause signal registration issues. The NextSeq 1000/2000 and the NovaSeq X Series sequence index 2 in the reverse-complement orientation, but DRAGEN requires index 2 to be entered in forward orientation, thus index 2 cannot *end* with CC (while index 1 cannot *start* with GG) in the sample sheet. This criteria is more relevant for lower plexity pools. Higher plexity pools are able to pass registration due to larger percentage of signal from neighboring clusters. Note that even optimally color-balanced pools can display base calling errors if the run is severely overloaded or underloaded. Libraries must be sequenced at their optimal loading concentration to ensure the best demultiplexing results. **Example Low-Plexity Index Adapter Combinations\*** * For 2-plex it may not be possible to have both green and blue representation in every cycle, but all recommended pairs have signal in the green channel (highlighted green) for every cycle. 2-plex examples below: ![](/files/51tARogjFWd3wmyHfEAe) * For 3-plex and above: recommended pooling combinations have representation in both green (C or T) and blue (C or A) channels. 3-plex examples below: ![](/files/JjxN6BOPcCYcGqNW2DbM) \*For more information on index selection for low-plexity pools, and additional low-plexity combinations of Illumina indexes, see the Illumina [Index Adapters Pooling Guide](https://support.illumina.com/downloads/index-adapters-pooling-guide-1000000041074.html) and the [Illumina Adapter Sequences](https://support.illumina.com/downloads/illumina-adapter-sequences-document-1000000002694.html) Guide. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #8422), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003035%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Index color balancing for the NextSeq 500/550 and MiniSeq systems When pooling libraries for sequencing on the NextSeq 500/550 and MiniSeq systems, it is important to select compatible index combinations, otherwise, the Index Read sequencing can fail due to cluster registration failures. This bulletin provides guidelines for pooling Illumina libraries on the NextSeq 500/550 and MiniSeq systems.\ **2-Channel Sequencing** NextSeq 500/550 and MiniSeq systems use two images to determine all four base calls, one red channel and one green channel. Rather than using a separate fluorescent dye for each base, 2-channel sequencing uses combinations of two fluorescent dyes: red for C, green for T, green and red for A, and no dye for G. ![](/files/PX9KiRFiKeyuzK5bkqBW) Figure 1: Two-channel SBS fluorescent imaging (false color image of the dyes is shown for illustration purposes). Accelerated detection of all four DNA bases is performed on the MiniSeq and NextSeq 500/550 series systems using two images to capture red and green wavelength bands. Clusters seen only in red or green images are identified as C and T bases, respectively. Clusters observed in both red and green images are identified as A bases, while unlabeled clusters are identified as G bases. **Index Considerations** * Index Reads must begin with at least one base other than G in either of the first two cycles. If an Index Read begins with two base calls of G, no signal intensity is generated, and cluster registration will fail. Signal must be present in either of the first 2 cycles to ensure demultiplexing performance. * Select index sequences that provide signal in at least one channel, preferably both channels, for every cycle. * Red channel - A or C * Green channel - A or T This base calling process ensures accuracy for data analysis. **Index Combinations Example** ![](/files/TSKhxwm546kAqFKUwbgY) Ideal index combinations: contain signal in both channels for every cycle. ![](/files/lF8NdWcJZnmestuBy1CC) Acceptable index combinations: have signal in only one channel, but there is still enough signal to sequence. ![](/files/XTCR7okNWFKDtnFzSePv) Unacceptable index combinations: will fail registration because the index read begins with 2 base calls of G and no signal intensity is generated. ![](/files/DWolDzuA5jGjTHWgkwla) More information about 2-channel sequencing can be found on the [2-Channel SBS Technology](https://sapac.illumina.com/science/technology/next-generation-sequencing/sequencing-technology/2-channel-sbs.html?langsel=/my/) web page[.](https://www.illumina.com/science/technology/next-generation-sequencing/sequencing-technology/2-channel-sbs.html) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1241), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001241%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Installing Reference Genomes on NovaSeq X Series Control Software v1.4 **Background** Certain DRAGEN Secondary Analysis workflows utilize reference Genomes for alignment and variant calling. These workflows require that the Genomes are installed onto the instrument so they are accessible by the DRAGEN Secondary Analysis. Due to the file size of the Genomes and disk space limitations on the NovaSeq X Series instrument, users are not able to install all available Genomes on the instrument. The following Table lists available packaged and individual Genomes, as well as the file sizes for each Genome. For installation instructions, see the [Software Updates](https://support-docs.illumina.com/IN/NovaSeqX/Content/SoftwareUpdates.htm) section of the NovaSeq X Series Product documentation. **Table 1**. Available packaged and individual reference v11 Genomes with disk space requirements for each. ![](/files/tOsSV11q0h7iy2QgcENp) **Table 2**: Available packaged and individual reference v10 Genomes with disk space requirements for each. ![](/files/KNVmnnqjrJ1WnAyiKhxJ) For an interactive reference Genomes checklist and disk space estimator, contact [Illumina Technical Support](https://www.illumina.com/company/contact-us.html#/united-states/technical-support). \ \ \
| | | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #10233), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000010233%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Instructions for thawing and storing NextSeq 500/550 reagents Illumina guarantees at least 3 months shelf life from the date of shipment. Reagent performance is guaranteed until the expiration date printed on the label, as long as the reagents are stored following Illumina recommendations. **Recommended storage conditions for NextSeq 500/550 consumables:**\ ![](/files/XYmBc0acC6qdhRoqDxhT) **Shipment Conditions** * NextSeq 500/550 v2.5 flow cells ship at ambient temperatures. Upon arrival, store flow cells at 2°C to 8°C. * NextSeq 500/550 reagent cartridge is shipped on dry ice. Upon arrival, store at -25°C to -15°C. * NextSeq 500/550 buffer cartridge is shipped at ambient temperatures. Upon arrival, store at 15°C to 30°C. **Box Dimensions:** * NextSeq 500/550 SBS Cartridge (-20°C): 12.3" x 10.25" x 2.9" * NextSeq 500/550 Accessory Box (-20°C): 5.68" x 3.59" x 2.12" * NextSeq 500/550 Flow Cell Box (4°C): 6.5" x 8.75" x 0.93" * NextSeq 500/550 Buffer Cartridge (Room Temp): 14.75" x 4.18" x 4.18" Note\*\*:\*\* Same for all NextSeq 500/550 kit types **To prepare the reagent cartridge:** * Thaw the reagent kit in a room temperature, deionized water bath for 60 minutes. * When water is added to the fill line on the cartridge, the cartridge stays at bottom of the water bath and does not float. * Once thawed, place on ice or set aside at 2°C to 8°C, and use as quickly as possible and within the same day. * Alternatively, thaw overnight at 2°C to 8°C, then store at 2°C to 8°C for up to 1 week. **To prepare the flow cell:** * Remove the flow cell package from 2°C to 8°C storage. * Set unwrapped flow cell package aside at room temperature for 30 minutes. * If the foil package is intact, the flow cell can remain at room temperature for up to 12 hours. * Avoid repeated cooling and warming of the flow cell. * When the flow cell is removed from foil (room temperature), the flow cell must be used right away for optimal performance, though can be used within a couple of hours. * Illumina does not recommend returning the flow cell to 2°C to 8°C storage after warming, as condensation may form, which can negatively impact run performance. This information is also available in video form. Search for Knowledge Base article [How to Prepare Reagents Pre-Run on the NextSeq 500/550 Video](https://knowledge.illumina.com/instrumentation/nextseq-500-550/instrumentation-nextseq-500-550-reference_material-list/000007450)[.](https://knowledge.illumina.com/instrumentation/nextseq-500-550/instrumentation-nextseq-500-550-reference_material-list/000007450) \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #1974), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001974%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | # Instrument Service Contract Plans Illumina Product Support Service Plans help maximize performance and productivity with reliable, high-quality results at various cost-effective levels. For the most up to date information and pricing, please reach out to your local Illumina sales representative. For help getting in touch with sales, see [Contact Illumina Sales](https://www.illumina.com/company/contact-us.html#/united-states/sales). A standard 1-year base warranty is included with every new Illumina instrument purchase, along with installation\* and basic applications trainings. Illumina also offers several tiered Service Plans to upgrade the base warranty to an enhanced service level or extend service coverage beyond the 1-year warranty. Below is a description of the current offerings for base warranty or service contract. ![](/files/wNM4DfLVxT8reOGNjG3x) **1-Year Base Warranty** * Instrument repair parts, labor, and travel. * 5 business day on-site response time target. * Reagent replacement due to instrument failures. * Hardware and Control Software updates. * Applications support. * 5 × 8 phone and email access to Technical Support (8 hours per day, Monday to Friday). **Bronze** * Instrument repair parts, labor, and travel. * 3 business day on-site response time target. * No reagent replacements due to instrument failures. * Applications support. * Hardware and Control Software updates. * 5 × 8 phone and email access to Technical Support (8 hours per day, Monday to Friday). **Silver** * Instrument repair parts, labor, and travel. * 2 business day on-site response time target. * Reagent replacements due to instrument failures. * 1 Annual Preventive Maintenance. * Applications support. * Hardware and Control Software updates. * 5 × 18 phone and email access to Technical Support (18 hours per day, Monday through Friday). **Gold** * Instrument repair parts, labor, and travel. * Next business day on-site response time target. * Reagent replacements due to instrument failures. * 1 Annual Preventive Maintenance. * 1 Operational Qualification (OQ) at Preventive Maintenance visit and after a qualified repair. * Applications support. * Hardware and Control Software updates. * 5 × 24 phone and email access to Technical Support. See [Illumina Instrument Service Plans](https://www.illumina.com/services/instrument-services-training/product-support-services/service-plans.html) for more information. \* The **MiSeq i100 Series** and **iSeq 100** are customer-installed in some Regions. \ \ \
| | | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | *For any feedback or questions regarding this article (Illumina Knowledge Article #3016), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000003016%20-%20Instrumentation%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* | --- [Next Page](/llms-full.txt/1)