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