bio-binning-qc SKILL.md skillA
bio-binning-qc from fmschulz/omics-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fmschulz/omics-skills/bio-binning-qc@git:20261001.bf5afd6Pins git:20261001.bf5afd6 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- fmschulz/omics-skills
- Path
skills/bio-binning-qc/SKILL.md- Versions recorded
- 6
- Latest version
- git:20261001.bf5afd6, committed Oct 1, 2026
- First version recorded
- Jul 11, 2026
- Size
- 5,691 bytes
- Repository stars
- 11
- License
- MIT
Bin metagenomic contigs with QuickBin and assess MAG quality with CheckM2, GUNC, EukCC, and GTDB-Tk. Use when binning an assembly or scoring bin completeness and contamination.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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](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](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: …
Read the whole file at its exact version.
How to install
mdr add fmschulz/omics-skills/bio-binning-qc@sha256:ac0d2ff8cf05fbd5The line at the top of this page pins the label git:20261001.bf5afd6, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_5rc66rlpjabw2gdy)
4 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jul 11, 2026 and Oct 1, 2026, about one every 16 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261001.bf5afd6 latest | 2026-10-01 | bf5afd6 | 5,691 B | A | view · diff |
| git:20260905.3e49039 | 2026-09-05 | 3e49039 | 4,568 B | A | view · diff |
| git:20260825.978bb0a | 2026-08-25 | 978bb0a | 4,412 B | A | view · diff |
| git:20260825.bd47e68 | 2026-08-25 | bd47e68 | 4,989 B | A | view · diff |
| git:20260712.3675171 | 2026-07-12 | 3675171 | 5,000 B | A | view · diff |
| git:20260711.5ae6f6f | 2026-07-11 | 5ae6f6f | 4,419 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (5691 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
fmschulz/omics-skills · 11 stars · license MIT · pushed 2026-10-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_5rc66rlpjabw2gdy GET https://markdownregistry.com/api/v1/resolve?ref=fmschulz/omics-skills/bio-binning-qc GET https://markdownregistry.com/api/v1/blob/ac0d2ff8cf05fbd5fe1bf2268fe78d1f8ae29f8095e915a0227b9bb4f521a93d
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.