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Illumina Infectious Disease Software
Illumina Connected Software
  • πŸ‘ΎIllumina Infectious Disease and Microbiology Software
  • DRAGEN Microbial Amplicon
    • ▢️DRAGEN Microbial Amplicon App Documentation
      • πŸŒ€How to start
      • Page
      • 🧬Custom reference
        • πŸ“„Reference BED file format
        • πŸ“„PCR Primer definition file formats
      • πŸ“‚Output files
      • πŸ“–Understanding the BaseSpace Reports
        • πŸ“„Summary
        • πŸ“„Sample Report
      • πŸ’ Pipeline Logic
      • ⭐Special considerations for amplicon detection
      • ❓Frequently Asked Questions (FAQ)
  • DRAGEN Targeted Microbial
    • ▢️DRAGEN Targeted Microbial App Documentation
      • πŸŒ€How to set up and run an analysis
      • 🧬Custom genomes and primer sets
        • πŸ“„Genome definition file formats
        • πŸ“„Primer definition file formats
      • βš™οΈApp Settings
      • πŸ“–Understanding the BaseSpace Reports
        • πŸ“„Summary Report
        • πŸ“„Result Reports
      • πŸ“‚Output files
      • πŸ’ 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
      • πŸŒ€How to set up and run an analysis
        • 🧬Custom reference FASTA and BED files
        • πŸ“„Microorganism Reporting File format
      • πŸ“‚Output files
        • πŸ“–Understanding the BaseSpace HTML reports
        • πŸ“–Report JSON format
      • πŸ’ Pipeline logic
      • ⭐Test information
        • πŸ“„RPIP
        • πŸ“„UPIP
        • πŸ“„RVOP/RVEK
        • πŸ“„VSP
        • πŸ“„VSP V2
        • πŸ“„Custom Panel
      • πŸ•΅οΈβ€β™€οΈScientific evidence
      • ❓Frequently Asked Questions (FAQ)
      • 🚩Release notes
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  1. DRAGEN Microbial Amplicon
  2. DRAGEN Microbial Amplicon App Documentation

How to start

PreviousDRAGEN Microbial Amplicon App DocumentationNextPage

Last updated 5 months ago

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  1. Launch the DRAGEN Microbial Amplicon BaseSpace application.

  2. Choose the analysis name and destination project to save results to.

  3. Choose either Biosample or Project as input method. Selecting Project will result in all biosamples in the selected project being analyzed.

  4. Choose the appropriate Amplicon Primer Set that matches the primer design used to prepare your samples or choose Custom to provide your own. See this to learn more about the custom option.

  5. If needed, uncheck the appropriate boxes to disable Pangolin and Nextclade analyses. These tools perform phylogenetic analysis and lineage assignment for SARS-CoV-2 (Pangolin) and other viruses (Nextclade). Depending on the chosen Amplicon Primer Set, these tools may not be applicable.

  6. If needed, expand the Advanced Workflow Settings box to change default settings. Click on the "i" circle next to each setting for more information.

  7. If needed, expand the Additional DRAGEN Command Line Arguments to provide additional arguments to default DRAGEN commands.

  8. Click β€œLaunch Application"

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