# Illumina Infectious Disease Software

## Illumina Infectious Disease Software

- [Illumina Infectious Disease and Microbiology Software](https://help.idm.illumina.com/readme.md): This page provides an overview of the software available on Illumina's cloud platforms
- [DRAGEN Microbial Amplicon App Documentation](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon.md)
- [How to start](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/start.md)
- [Custom reference](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/custom.md)
- [Reference FASTA](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/custom/fasta.md)
- [Reference BED](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/custom/bed.md)
- [PCR primer definition](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/custom/pcr-primer-definition.md)
- [Output files](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/output.md)
- [Understanding the BaseSpace reports](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/basespace-reports.md)
- [Summary](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/basespace-reports/summary.md)
- [Sample Report](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/basespace-reports/sample-report.md)
- [Pipeline Logic](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/pipeline.md)
- [Special considerations for amplicon detection](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/amplicon-detection.md)
- [Additional analysis](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/additional-analysis.md)
- [Frequently asked questions (FAQ)](https://help.idm.illumina.com/dragen-microbial-amplicon/dragen-microbial-amplicon/faq.md)
- [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)
- [DRAGEN Microbial Enrichment Plus App Documentation](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus.md)
- [How to set up and run an analysis](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis.md)
- [Custom reference FASTA and BED files](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis/custom-reference-fasta-and-bed-files.md)
- [Microorganism Reporting File format](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis/microorganism-reporting-file-format.md)
- [Output files](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files.md)
- [Understanding the BaseSpace HTML reports](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files/understanding-the-basespace-html-reports.md)
- [Report JSON format](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/output-files/report-json-format.md)
- [Pipeline logic](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/pipeline-logic.md)
- [Test information](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information.md)
- [RPIP](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/rpip.md)
- [UPIP](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/upip.md)
- [RVOP/RVEK](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/rvop-rvek.md)
- [VSP](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/vsp.md)
- [VSP V2](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/vsp-v2.md)
- [Custom Panel](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/test-information/custom-panel.md)
- [Scientific evidence](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/scientific-evidence.md)
- [Frequently Asked Questions (FAQ)](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/frequently-asked-questions-faq.md)
- [Release notes](https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/release-notes.md)
- [DRAGEN 16S Plus App Documentation](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus.md)
- [How to set up and run an analysis](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/how-to-set-up-and-run-an-analysis.md)
- [Custom database FASTA file format](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/how-to-set-up-and-run-an-analysis/custom-database-fasta-file-format.md)
- [Output files](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/output-files.md)
- [Understanding the BaseSpace HTML reports](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/output-files/understanding-the-basespace-html-reports.md)
- [Report JSON format](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/output-files/report-json-format.md)
- [Pipeline logic](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/pipeline-logic.md)
- [Test information](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/test-information.md)
- [Frequently Asked Questions (FAQ)](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/frequently-asked-questions-faq.md)
- [Release notes](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/release-notes.md)


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