> 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/dragen.md).

# DRAGEN

- [FAQ](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list.md)
- [Analysis options FAQ for Illumina Rapid RNA Kits](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list/000010217.md)
- [Are DRAGEN servers able to handle multiple users simultaneously?](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list/000006027.md)
- [DRAGEN Analysis Pipelines FAQ for Illumina Rapid RNA Kits](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list/000010218.md)
- [How is zygosity assigned for mitochondrial variant calls with DRAGEN?](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list/000007537.md)
- [How to enable DRAGEN to process multiple FASTQ files for the same subject?](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list/000006031.md)
- [Variant and Methylation calling FAQ for the Illumina 5-Base WGS and Enrichment kits](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list/000009952.md)
- [Reference Material](https://knowledge.illumina.com/software/dragen/software-dragen-reference_material-list.md)
- [Compatible callers for non-human references in the DRAGEN Germline App](https://knowledge.illumina.com/software/dragen/software-dragen-reference_material-list/000009848.md)
- [Download links for DRAGEN Reference genome FASTA files](https://knowledge.illumina.com/software/dragen/software-dragen-reference_material-list/000007409.md)
- [How to connect to the Java SOL on DRAGEN v3 Hardware](https://knowledge.illumina.com/software/dragen/software-dragen-reference_material-list/000009858.md)
- [Troubleshooting](https://knowledge.illumina.com/software/dragen/software-dragen-troubleshooting-list.md)
- [Instructions to back up DRAGEN license files when upgrading the operating system on a DRAGEN server](https://knowledge.illumina.com/software/dragen/software-dragen-troubleshooting-list/000008620.md)


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