# General

- [Troubleshooting](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list.md)
- [DRAGEN reference differences for on instrument and standalone analysis](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000009589.md)
- [Does the DRAGEN pipeline support VQSR (Variant Quality Score Recalibration)?](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000006139.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)
- [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 LRM analysis module not available at run start on NextSeq 500/550](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000001904.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)
- [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 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)
- [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)
- [Adapter trimming Why are adapter sequences trimmed from only the 3' ends of reads](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002905.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)
- [Different options/apps/pipelines available on the MiSeq i100, Nextseq2000, NovaSeqX, DRAGEN on BaseSpace, DRAGEN server and on Illumina Connected Analytics (ICA)](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000005165.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 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 convert a custom BED file to a manifest file for enrichment analysis](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002840.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 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)
- [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 on how to restart run upload to BaseSpace using BaseSpace Broker](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001811.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)
- [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 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)


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://knowledge.illumina.com/software/general.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.