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# 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:
### Input files:
* FASTQ files
* [User-defined microorganism reporting file in TSV or XLSX format](/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis/microorganism-reporting-file-format.md) (optional)
* [Custom reference FASTA file](/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis/custom-reference-fasta-and-bed-files.md) (if applicable)
* [Custom reference BED file](/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/how-to-set-up-and-run-an-analysis/custom-reference-fasta-and-bed-files.md) (if applicable)
### Demo Data:
The [DRAGEN Microbial Enrichment Plus Demo Project](https://basespace.illumina.com/s/T2YZsj1EPkzJ) 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.
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