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  • DRAGEN Microbial Amplicon
    • ▶️DRAGEN Microbial Amplicon App Documentation
      • 🌀How to start
      • Page
      • 🧬Custom reference
        • 📄Reference BED file format
        • 📄PCR Primer definition file formats
      • 📂Output files
      • 📖Understanding the BaseSpace Reports
        • 📄Summary
        • 📄Sample Report
      • 💠Pipeline Logic
      • ⭐Special considerations for amplicon detection
      • ❓Frequently Asked Questions (FAQ)
  • DRAGEN Targeted Microbial
    • ▶️DRAGEN Targeted Microbial App Documentation
      • 🌀How to set up and run an analysis
      • 🧬Custom genomes and primer sets
        • 📄Genome definition file formats
        • 📄Primer definition file formats
      • ⚙️App Settings
      • 📖Understanding the BaseSpace Reports
        • 📄Summary Report
        • 📄Result Reports
      • 📂Output files
      • 💠Pipeline Logic
      • ⭐Special considerations for amplicon sequencing with IMAP protocols
      • ❓Frequently Asked Questions (FAQ)
      • 🚩Known issues
  • DRAGEN Microbial Enrichment Plus
    • ▶️DRAGEN Microbial Enrichment Plus App Documentation
      • 🌀How to set up and run an analysis
        • 🧬Custom reference FASTA and BED files
        • 📄Microorganism Reporting File format
      • 📂Output files
        • 📖Understanding the BaseSpace HTML reports
        • 📖Report JSON format
      • 💠Pipeline logic
      • ⭐Test information
        • 📄RPIP
        • 📄UPIP
        • 📄RVOP/RVEK
        • 📄VSP
        • 📄VSP V2
        • 📄Custom Panel
      • 🕵️‍♀️Scientific evidence
      • ❓Frequently Asked Questions (FAQ)
      • 🚩Release notes
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  1. DRAGEN Microbial Enrichment Plus
  2. DRAGEN Microbial Enrichment Plus App Documentation

Pipeline logic

Pipeline steps

Step
Description
Notes
RPIP
UPIP
RVOP/RVEK
VSP
VSP V2
Custom Panel

Read QC

Low-quality bases are trimmed from the ends of each read. After trimming, the read is discarded if fewer than 50% of its bases have a quality score greater or equal to q20, the read is shorter than 32 bp, or the read has 5 or more ambiguous bases. It is assumed that appropriate adapter trimming has already been performed.

Optional

X

X

X

X

X

X

Dehosting

Human read removal using the DRAGEN Kmer Classifier

X

X

X

X

X

X

Sample QC

Sample composition and enrichment factor calculations

Internal control required to calculate the enrichment factor

X

X

X

Microorganism classification

Pre-alignment filtering step

Configurable sensitivity

X

X

X

Microorganism detection

Reference alignment, consensus sequence generation, variant calling

X

X

X

X

X

X

Microorganism quantification

Absolute copies/mL calculation

Quantitative internal control and concentration required

X

X

X

Microorganism reporting thresholds

Proprietary algorithms or user-defined reporting logic

X

X

X

X

X

Bacterial AMR marker analysis

Nucleotide and protein alignment, consensus sequence generation, variant calling and annotation

X

X

Viral AMR marker analysis

Variant calling and annotation

X

X

X

X

Viral clade and lineage prediction

Pangolin, Nextclade

X

X

X

X

Result filters

User-specified filters applied

X

X

X

X

X

Reporting - Analysis level

XLSX, HTML, ZIP

X

X

X

X

X

X

Reporting - Sample level

JSON, HTML, FASTA (consensus sequences), VCF (viral variants)

X

X

X

X

X

X

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Last updated 6 months ago

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