majiayu000 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
- 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).
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