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claude-codescience

Claude-skill-registry bio-binning-qc

Perform metagenomic binning, refinement, and QC with completeness/contamination checks.

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 "$T/skills/data/bio-binning-qc" ~/.claude/skills/majiayu000-claude-skill-registry-bio-binning-qc && rm -rf "$T"
manifest: skills/data/bio-binning-qc/SKILL.md
tags
#metagenomic-binning#qc-analysis#checkm2#eukcc#gunc#domain-classification
source content

Bio Binning QC

When to use

  • Perform metagenomic binning, refinement, and QC with completeness/contamination checks.

Prerequisites

  • Tools installed via pixi (see pixi.toml).
  • Reference DB root: /media/shared-expansion/db/ (wsu; override per machine branch).
  • Coverage/depth tables or reads available to compute coverage.

Inputs

  • contigs.fasta
  • coverage.tsv (per-sample depth table)

Outputs

  • results/bio-binning-qc/bins/
  • results/bio-binning-qc/bin_metrics.tsv
  • results/bio-binning-qc/bin_qc_report.html
  • results/bio-binning-qc/logs/

Steps

  1. Compute depth/coverage per sample.
  2. Run multiple binners (MetaBAT2, SemiBin2, QuickBin).
  3. Classify bins by domain (bacteria/archaea vs eukaryotes).
  4. Run domain-specific QC:
    • CheckM2 for bacterial and archaeal bins
    • EukCC for eukaryotic bins
    • GUNC for contamination detection (all domains).

QC gates

  • Completeness and contamination meet project thresholds.
  • Chimera and 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 and coverage.tsv are non-empty.
  • Verify reference DBs for QC tools exist under the reference root.

Tools

  • coverm v0.7.0 (coverage computation)
  • metabat2 v2.18 (binning)
  • semibin2 v2.2.1 (binning)
  • bbtools (quickbin) v39.52 (binning)
  • checkm2 v1.0.2 (QC for bacteria/archaea)
  • eukcc v2.x (QC for eukaryotes)
  • gunc v1.0.6 (contamination detection)

Paper summaries (2023-2025)

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

Tool documentation

  • CoverM - Coverage and depth calculation
  • MetaBAT2 - Metagenomic binning
  • SemiBin2 - Deep learning-based metagenomic binning
  • QuickBin - Fast binning with BBTools
  • CheckM2 - Quality assessment for bacterial and archaeal genomes
  • EukCC - Quality assessment for eukaryotic genomes
  • GUNC - Detection of chimerism and contamination

References

  • See ../bio-skills-references.md