What is bio-binning-qc?

A workflow for grouping assembled metagenomic DNA fragments into draft genomes and checking their quality. Metagenomics studies genetic material collected from mixed communities of organisms.

It helps calculate coverage, create and refine bins, screen their likely domain, assign taxonomy, and assess completeness and contamination.

It helps separate mixed assemblies into genome bins and identify problems such as missing sequence, contamination, or inconsistent bin contents.

bio-binning-qc — Skill for Claude Code by fmschulz

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add fmschulz/omics-skills --skill bio-binning-qc

Clone the repo

git clone --depth 1 https://github.com/fmschulz/omics-skills

Made for: Claude Code.

Or install omics-skills, the plugin that ships this one along with the rest of its 34 skills, 4 agents.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-binning-qc/github.svg)](https://agentmods.dev/skills/fmschulz/omics-skills/bio-binning-qc)

Your own site

<a href="https://agentmods.dev/skills/fmschulz/omics-skills/bio-binning-qc"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-binning-qc/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/fmschulz/omics-skills/bio-binning-qc"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-binning-qc.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 37 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 1,174 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00037	$0.01174
Opus 5	$0.00018	$0.00587
Sonnet 5	$0.00007	$0.00235
Haiku 4.5	$0.00004	$0.00117

Measured 3d ago against content hash 35738593fcd1, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

bio-binning-qc scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 3d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/build_bin_qc_tables.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/bio-binning-qc/SKILL.md · 69 lines

How it starts

The opening of the file, as written. The whole thing — 69 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Bio Binning QC

Perform metagenomic binning, refinement, and QC with completeness/contamination checks.

Instructions

Tool guides and versions: docs/README.md.

Compute per-sample depth/coverage with CoverM v0.7.0+ (or BBMap for short reads, minimap2 for long reads).
Bin contigs with QuickBin through Bryce Foster's official BBTools container (bryce911/bbtools:39.85; 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 v2.3.0+ instead — self-supervised contrastive learning with CUDA-backed PyTorch. MetaBAT2 v2.18+ is kept only as a legacy fallback for reproducing prior pipelines.
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.
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.
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 v1.0.6+ for bacterial and archaeal bins only; treat it as a complement to CheckM2 for chimerism detection. Do not apply GUNC to eukaryotic bins.
Normalize routed outputs with scripts/build_bin_qc_tables.py. The join rejects GUNC rows for non-prokaryotic routes and refuses prokaryotic or eukaryotic bins that lack their domain-specific QC/taxonomy outputs.

Read the full file on GitHub · 69 lines

Files

What ships with it

14 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

3d ago Changed 35738593fcd1
10d ago First seen · 69 lines · 37 tokens per session scan A 21062088ee58

Subscribe to this mod's changes

bio-binning-qc is a skill published in the GitHub repository fmschulz/omics-skills (7 stars, last pushed 4d ago), licensed MIT. It adds 37 tokens to every session and 1,174 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

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