> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/software/general.md).

# General

- [Troubleshooting](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list.md)
- [Creating custom reference genomes (non human) to use with DRAGEN apps on BaseSpace Sequence Hub](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000007488.md)
- [DRAGEN reference differences for on instrument and standalone analysis](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000009589.md)
- [How to demultiplex an incomplete run using bcl2fastq2 and BCL Convert](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000003577.md)
- [How to generate FASTQs from an incomplete run in Local Run Manager](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000001807.md)
- [How to troubleshoot a "None of the specified endpoints were reachable" error in Local Run Manager](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000001217.md)
- [How to troubleshoot barcode collision and not enough hamming distance errors when demultiplexing runs with BCL Convert and bcl2fastq2](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000002326.md)
- [Illumina Connected Analytics (ICA) kernel cannot connect in a Bench Workspaces](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000007769.md)
- [Options for demultiplexing libraries with different index lengths in the same sequencing run](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000005982.md)
- [Sample specific nucleotide error bias estimation filter and systematic noise filter in DRAGEN](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000006989.md)
- [Troubleshooting demultiplexing issues for local DRAGEN analysis onboard the NextSeq 1000/2000](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000003817.md)
- [Troubleshooting demultiplexing issues using BaseSpace Sequence Hub and bcl2fastq2 v2.17+](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000002875.md)
- [Troubleshooting demultiplexing issues using Local Run Manager](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000002862.md)
- [Troubleshooting demultiplexing issues using MiSeq Reporter](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000002227.md)
- [Unlocking an account or resetting the password on Local Run Manager version 4](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000009008.md)
- [FAQ](https://knowledge.illumina.com/software/general/software-general-faq-list.md)
- [Analysis FAQ for the TruPath Genome assay](https://knowledge.illumina.com/software/general/software-general-faq-list/000010170.md)
- [Can BaseSpace files be transferred directly to AWS (Amazon Web Services)?](https://knowledge.illumina.com/software/general/software-general-faq-list/000002832.md)
- [Can a run be started on the NovaSeq X/X Plus while an analysis is ongoing?](https://knowledge.illumina.com/software/general/software-general-faq-list/000008267.md)
- [Does TruSight Oncology 500 (TSO500) use a segmentation algorithm to determine the genomic coordinates of a copy number call?](https://knowledge.illumina.com/software/general/software-general-faq-list/000009436.md)
- [How is zygosity assigned for mitochondrial variant calls with DRAGEN?](https://knowledge.illumina.com/software/general/software-general-faq-list/000007537.md)
- [How to invite users to a Project in Illumina Connected Analytics v2](https://knowledge.illumina.com/software/general/software-general-faq-list/000007549.md)
- [How to requeue FASTQ Generation using BCL Convert on BaseSpace](https://knowledge.illumina.com/software/general/software-general-faq-list/000006472.md)
- [How to run the DRAGEN MSI Pipeline](https://knowledge.illumina.com/software/general/software-general-faq-list/000007508.md)
- [How to use the 'OverrideCycles' setting in the Run Planning User Interface](https://knowledge.illumina.com/software/general/software-general-faq-list/000005671.md)
- [Is there a certain number of times that users can requeue local analysis?](https://knowledge.illumina.com/software/general/software-general-faq-list/000007161.md)
- [MiSeq Reporter common questions](https://knowledge.illumina.com/software/general/software-general-faq-list/000002240.md)
- [When will FASTQ files be N masked in Local Run Manager, MiSeq Reporter, bcl2fastq, and BCL Convert?](https://knowledge.illumina.com/software/general/software-general-faq-list/000003633.md)
- [Why are underscores in sample names changed to dashes in the FASTQ file names?](https://knowledge.illumina.com/software/general/software-general-faq-list/000003636.md)
- [Reference Material](https://knowledge.illumina.com/software/general/software-general-reference_material-list.md)
- [BCL Convert and index UMIs How to demultiplex samples and output a UMI FASTQ](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007337.md)
- [BaseSpace FASTQ Processing Tools for Data Analysis Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008085.md)
- [Creating a custom genome for NovaSeq X Series](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000009590.md)
- [DRAGEN Enrichment App in BaseSpace](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003686.md)
- [DRAGEN Metagenomics Pipeline in BaseSpace general information](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003688.md)
- [FASTQ文件解读](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007412.md)
- [Generating checksums for a file](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008482.md)
- [Guidelines for reverse complementing i5 sequences for demultiplexing](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001800.md)
- [How to Add a User to Illumina Connected Multiomics Domain and Workgroup](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000010147.md)
- [How to Specify Adapters for Trimming in Local Run Manager](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003678.md)
- [How to add a Custom Reference Genome in Local Run Manager](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002685.md)
- [How to avoid Ns in small RNA or short reads when running BCL Convert](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000009157.md)
- [How to concatenate the FASTQ files from different lanes](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002035.md)
- [How to connect remotely to Local Run Manager v4 on instrument](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002323.md)
- [How to download only FASTQs from a BaseSpace project using BaseSpace CLI](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003376.md)
- [How to edit a sample sheet and requeue an analysis in BaseSpace Sequence Hub](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001321.md)
- [How to generate FASTQ files for index reads in MiSeq Reporter](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001326.md)
- [How to generate FASTQ files from an incomplete run in MiSeq Reporter](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001325.md)
- [How to realign a CRAM file to a new reference with DRAGEN](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007021.md)
- [How to requeue analysis of a run with MiSeq Reporter](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001782.md)
- [How to share BaseSpace Sequence Hub sequencing data from enterprise domain to public domain](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001666.md)
- [How to unlock BioSamples in BaseSpace using BaseSpace Command Line Interface (CLI)](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000005845.md)
- [How to use Exome 2.5 Panel of Normals reference for germline deletion/duplication analysis](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007918.md)
- [How to use a custom library prep kit in Local Run Manager v2](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001317.md)
- [How to use custom library prep and index kits with Local Run Manager v3 and v4](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000005897.md)
- [Illumina DRAGEN Bio IT Platform What is new with version 3.10 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008073.md)
- [Illumina DRAGEN Bio IT Platform What is new with version 3.9 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008075.md)
- [Illumina DRAGEN Bio IT Platform Ultra Rapid Analysis of Next Generation Data Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008091.md)
- [Illumina DRAGEN Bio IT Platform What is new with version 3.5 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008088.md)
- [Illumina DRAGEN Bio IT Platform What is new with version 3.6 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008083.md)
- [Illumina DRAGEN Bio IT Platform What is new with version 3.7 Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008086.md)
- [Illumina DRAGEN Bio IT Platform What is new with version 3.8 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008084.md)
- [Illumina DRAGEN v4.0 Unlock the Full Potential of Genomics Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008072.md)
- [Information on leading r for UMIs when demultiplexing NextSeq 1000/2000 or NovaSeq X series data with BCL Convert](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007945.md)
- [Instructions for using BaseSpace CLI on Windows to upload runs](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007950.md)
- [Investigation of Log4j Vulnerability status for Illumina off instrument software products](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000006344.md)
- [Investigation of Log4j Vulnerability with the Illumina DRAGEN Bio IT Platform](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000006340.md)
- [Investigation of Log4j Vulnerability](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000006335.md)
- [Local Run Manager How to create FASTQ files for index reads](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001323.md)
- [Maximum number of cycles for index reads on the NovaSeq X Series](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008417.md)
- [Metagenomic Sequencing Introduction to Data Analysis Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007979.md)
- [NextSeq 1000/2000 Introduction to Analysis with DRAGEN Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008076.md)
- [Sequencing Data Analysis Introduction to Key Concepts Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007978.md)
- [Trimming T overhang options for Illumina Stranded mRNA and Illumina Stranded Total RNA workflows](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003227.md)
- [TruSight Oncology 500 (TSO500) High Throughput Sample Sheet templates link](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003524.md)
- [TruSight Oncology 500 Assays and Analysis Options](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003812.md)
- [Upgrading from bcl2fastq to BCL Convert](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003710.md)
- [Using an N wildcard in index sequences in different Illumina FASTQ generation software](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003560.md)
- [Which orientation are the indexes in Top\_Unknown\_Barcodes output from BclConvert?](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000005078.md)
- [Why is allowing mismatches when demultiplexing desirable?](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007484.md)


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