▶️DRAGEN Microbial Enrichment Plus App Documentation

Overview

Summary:

DRAGEN Microbial Enrichment Plus offers a dedicated informatics solution with flexible analysis options for Illumina Infectious Disease and Microbiology target-capture enrichment panel kits. The app delivers easy-to-use, powerful secondary analysis of Illumina sequencing data, with workflows for sample QC, viral WGS (whole-genome sequencing), pathogen detection and quantification, and antimicrobial resistance (AMR) marker profiling. It also supports user-defined microorganism reporting thresholds and custom reference sequence analysis.

Supported hybrid-capture enrichment panels:

Product Page	Panel Summary
Illumina Respiratory Pathogen ID/AMR Enrichment Panel Kit (RPIP)	RPIP_6-3-0_Panel_Summary.xlsx
Illumina Urinary Pathogen ID/AMR Enrichment Panel Kit (UPIP)	UPIP_8-4-0_Panel_Summary.xlsx
Illumina Respiratory Virus Oligo Panel / Respiratory Virus Enrichment Kit (RVOP / RVEK)	RVOP_2-3-0_Panel_Summary.xlsx
Illumina Viral Surveillance Panel (VSP)	VSP_2-3-0_Panel_Summary.xlsx
Illumina Viral Surveillance Panel V2 (VSP V2)	VSPV2_2-3-0_Panel_Summary.xlsx

Input files:

• FASTQ files

• User-defined microorganism reporting file in TSV or XLSX format (optional)

• Custom reference FASTA file (if applicable)

• Custom reference BED file (if applicable)

Demo Data:

The [DRAGEN Microbial Enrichment Plus Demo Project] includes external control, contrived, and environmental samples prepared using the RPIP, UPIP, RVOP, VSP, and VSP V2 target-capture enrichment kits. Example custom reference sequence FASTA and BED files are also included.

Analysis Pipeline:

(all panels except where noted, (*) indicates applicable to custom reference sequence analysis)

1. Read QC* (optional)

2. Dehosting* (human read removal)

3. Sample QC (sample composition and enrichment factor calculations. Internal control required to calculate the enrichment factor) – RPIP, UPIP, VSP V2

4. Microorganism classification (configurable sensitivity) - RVOP, VSP, VSP V2

5. Microorganism detection (alignment, consensus generation, variant calling)

6. Microorganism quantification (quantitative internal control required) – RPIP, UPIP, VSP V2

7. Microorganism reporting thresholds (proprietary algorithms or user-defined reporting logic)

8. Bacterial AMR marker analysis (nucleotide and protein alignment, consensus generation, variant calling and annotation) – RPIP, UPIP

9. Viral AMR marker analysis (variant calling and annotation) – RPIP, RVOP, VSP, VSP V2

10. Viral clade and lineage prediction (Pangolin, Nextclade) – RPIP, RVOP, VSP, VSP V2

11. Result filters (user-specified filters applied)

12. Reporting*

Output files:

• Analysis-level outputs: XLSX, HTML, ZIP

• Sample-level outputs: JSON, HTML, FASTA (consensus sequences), VCF (viral variants)

Important Notes:

DRAGEN Microbial Enrichment Plus is a secondary analysis tool for research use only. Further interpretation, statistical analysis, and downstream analysis of results may be necessary.

For Research Use Only. Not for use in diagnostic procedures.