ViralUnity
  • Installation
    • Install from PyPI (recommended)
    • Clone and create the environment
    • Troubleshooting
      • CreateCondaEnvironmentException with a repodata_shards.msgpack.zst 404
    • Verify the installation
    • First-time environment setup
    • Development install
  • Tutorial
    • Pick a pipeline
    • How to read this tutorial
      • Setup
        • 1. Install ViralUnity
        • 1b. Build per-rule environments
        • 1c. Download the example data
        • 2. Generate sample sheets
        • 3. Decide which databases you need
        • 4. Download the metagenomic databases
        • 5. Verify the setup
      • Consensus pipeline tutorial
        • When to use it
        • What it does
        • Worked example 1 — Illumina (SARS-CoV-2 amplicon)
        • Worked example 2 — Nanopore (SARS-CoV-2)
        • Segmented viruses
        • Tuning consensus quality
        • Common pitfalls
        • Reference
      • Metagenomics pipeline tutorial
        • When to use it
        • What it does
        • Decision matrix — what to turn on
        • Worked example — Illumina, built up incrementally
        • Nanopore variant
        • Understanding the filters
        • Reference assembly under the hood
        • Tuning knobs
        • Common pitfalls
        • Reference
    • About the example data
    • Further reading
  • Usage Overview
    • General Workflow
  • Commands Reference
    • viralunity setup
      • Options
      • Examples
    • viralunity create-samplesheet
      • Options
      • Output format
      • Examples
    • viralunity consensus
      • Options — shared (both data types)
      • Input integrity validation
      • Options — Illumina only
      • Options — Nanopore only
      • Examples
    • viralunity meta
      • Pipeline overview (Illumina)
      • Pipeline overview (Nanopore)
      • Options — shared (both data types)
      • Options — Illumina only (fastp QC)
      • Options — Nanopore only (polishing)
      • Examples
      • Krona outputs (raw vs. filtered)
      • Taxonomic false-positive filters (optional)
    • viralunity get-databases
      • kraken2 — Kraken2 pre-built index
      • krona — Krona taxonomy
      • taxdump — NCBI taxdump
      • diamond — Diamond protein database
      • clean-protein-fasta — Strip nucleotide records from a protein FASTA
      • nr — NCBI nr database for NR validation
      • virus-genome — Viral genomes database
      • host-genome — Host genome download
      • deacon-index — Pre-built Deacon index
      • Download all databases at once
    • viralunity build-deacon-index
    • Configuration file overrides
    • Per-rule CPU and RAM overrides
  • Architecture
    • Data flow
    • Module map
    • The config is the contract
    • Workflow selection
  • Embedding ViralUnity in a service
    • Calling the pipeline
    • Per-job isolation (required)
    • Input contract (enforce on untrusted uploads)
    • Observability
    • Structured errors
    • Provenance
  • Output Layout
    • Consensus pipeline (viralunity consensus)
      • Key files
    • Metagenomics pipeline (viralunity meta)
      • Per-rank output layout
      • The taxa-summary filename chain (internal, under <track>/summaries/full/)
      • Key files
  • Interactive HTML Report
    • What it shows
    • Regenerating the report
    • Disabling the report
  • Notes
    • Negative-control enrichment filter
    • Segmented viruses
    • Nanopore data
    • Reference header sanitization
    • Dynamic reference assembly
      • How it works
      • Reference selection strategies
        • --reference-selection-strategy taxid (default)
        • --reference-selection-strategy similarity
      • Strategy comparison
      • Required databases
    • Running tests
  • Citation
    • ViralUnity
    • Dependencies
ViralUnity
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