Bio Binning QC
Perform metagenomic binning, refinement, and QC with completeness/contamination checks.
Instructions
- Compute depth/coverage per sample.
- Run multiple binners (MetaBAT2, SemiBin2, QuickBin).
- Classify bins by domain (bacteria/archaea vs eukaryotes).
- Run domain-specific QC:
- CheckM2 for bacterial and archaeal bins
- EukCC for eukaryotic bins
- 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.mdfor 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.