bio-binning-qc
Perform metagenomic binning with QuickBin, refinement, and QC with completeness/contamination checks.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-binning-qc --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Bio Binning QC Perform metagenomic binning, refinement, and QC with completeness/contamination checks. ## Instructions 1. Compute per-sample depth/coverage with CoverM v0.7.0+ (or BBMap for short reads, minimap2 for long reads). 2. Bin contigs with **QuickBin** through Bryce Foster's official BBTools container (`bryce911/bbtools:39.84`; record digest when pulled). QuickBin is high-fidelity, CheckM2-agnostic, and scales well on both short-read and long-read assemblies. On a GPU node, run **SemiBin2 v2.2.1+** instead — self-supervised contrastive learning with CUDA-backed PyTorch. MetaBAT2 v2.15+ is kept only as a legacy fallback for reproducing prior pipelines. 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 eukary
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Expected input layout
- Troubleshooting
What does the bio-binning-qc skill do?
Perform metagenomic binning with QuickBin, refinement, and QC with completeness/contamination checks.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-binning-qc --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.