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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 Amplicon
  2. DRAGEN Microbial Amplicon App Documentation

Pipeline Logic

PreviousSample ReportNextSpecial considerations for amplicon detection

Last updated 6 months ago

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Steps

Step
Module/Script
Run

QC

trimmomatic

Always

Primer trimming (on FASTQ)

trimmomatic

If assembly is to run

Remove off-target reads

DRAGEN

If checked in Input Form

Assembly

MEGAHIT

If reference FASTA and BED files imply more than one genome as reference

Contig clustering

CD-HIT

If assembly ran

Reference selection

custom script

If assembly ran, otherwise input reference database is used as is

Map/Align

DRAGEN

If at least one reference sequence is generated

Post-facto primer trimming (on BAM)

custom script

If Map/Align ran and primer set exists

Sample filtering based on amplicon coverage

custom script

If Map/Align ran and primer set exists

Variant calling

DRAGEN

If Map/Align ran and sample passed filter above

Consensus sequence generation

custom script

If Map/Align ran and sample passed filter above

Outcomes

Status
Level
Outcome

Completed successfully

Pipeline

Exit with all applicable output files

Custom files are not formatted correctly

Pipeline

Exit early with error

No remaining reads after preprocessing

Sample

Exit early with a report of read counts

No contig generated

Sample

Exit early with a report of read counts

No reference found after assembly

Sample

Exit early with a report of read counts and contig FASTA

None of the primers provided in custom primer definition file align to selected reference sequences

Sample

Skip post-factor primer trimming and sample filtering based on amplicon coverage for this sample

Insufficient amplicon coverage

Sample

Exit early before variant calling and consensus sequence generation

▶️
💠
Control and data flow diagram for the DRAGEN Microbial Amplicon app. Not all steps shown may be run depending on user inputs and pipeline outcome