Bio Binning QC

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

Instructions

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:
5. CheckM2 for bacterial and archaeal bins
6. EukCC for eukaryotic bins
7. GUNC for contamination detection (all domains).

Quick Reference

Task	Action
Run workflow	Follow the steps in this skill and capture outputs.
Validate inputs	Confirm required inputs and reference data exist.
Review outputs	Inspect reports and QC gates before proceeding.
Tool docs	See docs/README.md.
References	- See ../bio-skills-references.md

Input Requirements

Prerequisites:

• Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
• Reference DB root: set BIO_DB_ROOT (default /media/shared-expansion/db/ on WSU).
• Coverage/depth tables or reads available to compute coverage. Inputs:
• contigs.fasta
• coverage.tsv (per-sample depth table)

Output

• 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/

Quality 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.
• Verify contigs.fasta and coverage.tsv are non-empty.
• Verify reference DBs for QC tools exist under the reference root.

Examples

Example 1: Expected input layout

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

Troubleshooting

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.