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

# DRAGEN Targeted Microbial

- [DRAGEN Targeted Microbial App Documentation](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial.md)
- [How to set up and run an analysis](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/setting-up-an-analysis.md)
- [Custom genomes and primer sets](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/custom-genomes-and-primer-sets.md)
- [Genome definition file formats](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/custom-genomes-and-primer-sets/genome-definition-file-formats.md)
- [Primer definition file formats](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/custom-genomes-and-primer-sets/primer-definition-file-formats.md)
- [App Settings](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/settings.md): Describes the controls on the Input Form and their function
- [Understanding the BaseSpace Reports](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/understanding-the-basespace-reports.md): Brief description of Summary and Result reports and an explanation of their contents
- [Summary Report](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/understanding-the-basespace-reports/summary-report.md): Describes the report that can be viewed from the Summary link on the Reports tab of a completed analysis.
- [Result Reports](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/understanding-the-basespace-reports/result-reports.md): Describes the reports that can be viewed from the individual sample links on the left side of the reports tab or by clicking on sample names in the Metrics by sample table.
- [Output files](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/output-files.md)
- [Pipeline Logic](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/pipeline-logic.md): Descriptions of the logic underlying the DRAGEN Targeted Microbial analysis pipeline
- [Special considerations for amplicon sequencing with IMAP protocols](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/special-considerations-for-amplicon-sequencing-with-imap-protocols.md)
- [Frequently Asked Questions (FAQ)](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/frequently-asked-questions-faq.md)
- [Known issues](https://help.idm.illumina.com/dragen-targeted-microbial/dragen-targeted-microbial/known-issues.md)


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