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Claude-skill-registry bio-viromics

Detect, classify, and QC viral contigs.

install
source · Clone the upstream repo
git clone https://github.com/majiayu000/claude-skill-registry
Claude Code · Install into ~/.claude/skills/
T=$(mktemp -d) && git clone --depth=1 https://github.com/majiayu000/claude-skill-registry "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/data/bio-viromics" ~/.claude/skills/majiayu000-claude-skill-registry-bio-viromics && rm -rf "$T"
manifest: skills/data/bio-viromics/SKILL.md
tags
#viral-detection#taxonomic-classification#genome-quality#contig-analysis#vcontact3#checkv
source content

Bio Viromics

When to use

  • Detect, classify, and QC viral contigs.

Prerequisites

  • Tools installed via pixi (see pixi.toml).
  • Reference DB root: /media/shared-expansion/db/ (wsu; override per machine branch).
  • Input contigs are available.

Inputs

  • contigs.fasta

Outputs

  • results/bio-viromics/viral_contigs.fasta
  • results/bio-viromics/checkv_results/
  • results/bio-viromics/vcontact3_results/
  • results/bio-viromics/viral_taxonomy.tsv
  • results/bio-viromics/genome_clusters.tsv
  • results/bio-viromics/viromics_report.md
  • results/bio-viromics/logs/

Steps

  1. Run virus detection (geNomad).
  2. Run CheckV for completeness/contamination.
  3. Assign taxonomy and cluster genomes (vConTACT3 for hierarchical classification and gene-sharing network analysis).

QC gates

  • CheckV quality thresholds meet project standards.
  • Contamination flags are below thresholds.
  • On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.

Validation

  • Verify contigs.fasta is non-empty.
  • Verify viral reference DBs exist under the reference root.

Tools

  • genomad v1.11.2
  • checkv v1.0.3
  • vcontact3 v3.0.1
  • gvclass v1.2.0 (internal build tag)

Paper summaries (2023-2025)

  • summaries/ (include example use cases and tool settings used)

Tool documentation

  • geNomad - Viral sequence identification and classification
  • CheckV - Viral genome quality assessment
  • vConTACT3 - Viral taxonomy and clustering via gene-sharing networks
  • GVClass - Giant virus classification

References

  • See ../bio-skills-references.md