bio-binning-qc

Bio Binning QC

Bin metagenomic contigs, route bins by domain, run domain-specific quality checks, and join the results into normalized tables.

Instructions

Tool guides and versions: docs/README.md.

1. Map each sample's reads back to the assembly (BBMap or bwa-mem2 for short reads, minimap2 for long reads; see /bio-reads-qc-mapping), then compute per-sample contig depth from the sorted BAMs with CoverM v0.7.0+.
2. Bin contigs with QuickBin from Bryce Foster's BBTools container (bryce911/bbtools:39.85; record the digest when pulled). QuickBin is the default for short-read and long-read assemblies (docs/quickbin.md). On a CUDA GPU node, SemiBin2 v2.3.0+ is the alternative. Use MetaBAT2 v2.18+ only to reproduce a prior pipeline.
3. Run /tracking-taxonomy-updates for BBTools-container QuickClade domain triage on the bin directory and the source assembly with percontig. Persist the per-contig screen so mixed bins are visible.
4. Route bins by the QuickClade domain screen:
   • Bacteria or Archaea -> run GTDB-Tk taxonomy assignment. If the GTDB-Tk reference package is missing, set it up under $BIO_DB_ROOT, export GTDBTK_DATA_PATH, run gtdbtk check_install, and record the release before classification.
   • Eukaryota -> run EukCC v2.1.3+ for eukaryotic bins.
   • Viral or virus-like -> remove from MAG QC and route candidate contigs/genomes to /bio-viromics; use vConTACT3 for phage/prokaryotic-virus evidence and GVClass for giant-virus/Nucleocytoviricota candidates.
   • Mixed or low-confidence -> flag as potential chimeras and inspect per-contig assignments before QC scoring.
5. Run domain-specific QC:
   • CheckM2 v1.1.0+ for bacterial and archaeal bins (v1.1.0 is a breaking upgrade: update the pinned Pixi environment and refresh the DIAMOND v3 database from Zenodo DOI 10.5281/zenodo.14897628).
   • EukCC v2.1.3+ for eukaryotic bins.
   • GUNC v1.1.0+ (needed for the progenomes_3 and gtdb_214 databases) for bacterial and archaeal bins only, as a chimerism check next to CheckM2. Do not apply GUNC to eukaryotic bins. gunc run reads .fa files from --input_dir by default; set --file_suffix to match other bin suffixes.
6. Normalize routed outputs with scripts/build_bin_qc_tables.py. The join rejects GUNC rows for non-prokaryotic routes, refuses prokaryotic or eukaryotic bins that lack their domain-specific QC or taxonomy outputs, and refuses to overwrite existing outputs. Accepted routes are prokaryote, eukaryote, prokaryotic_virus, giant_virus, and manual_review.