bio-viromics SKILL.md skillA
bio-viromics 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-viromics@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-viromics/SKILL.md- Versions recorded
- 6
- Latest version
- git:20261001.bf5afd6, committed Oct 1, 2026
- First version recorded
- Jul 12, 2026
- Size
- 9,118 bytes
- Repository stars
- 11
- License
- MIT
Detect, QC, and classify viral contigs with geNomad, CheckV, vConTACT3, and GVClass. Use when finding viruses in assemblies, grading viral genomes, or assigning phage or giant-virus taxonomy.
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 Viromics Detect, quality-check, and classify viral contigs, then compare each viral genome against a literature-derived reference set. ## Instructions Tool guides, versions, and verified flags: [docs/README.md](docs/README.md). Run geNomad, CheckV, GVClass, and vConTACT3 on a workstation or compute node, never on a login node. Pass an explicit thread count to each tool (`-t`). Without it, geNomad and CheckV use every CPU available to the process, and vConTACT3 uses every CPU on the host, even inside a smaller Slurm allocation. On HPC, submit through `sbatch` with CPUs matched to that thread count and follow the site's account and partition rules. 1. Start from `/tracking-taxonomy-updates` QuickClade domain routing when assemblies, MAGs, genomes, or contigs have not been screened. Viral, virus-like, mixed, or low-confidence contigs enter this skill; bacterial, archaeal, and eukaryotic rows stay on their domain routes unless later evidence contradicts the triage. …
Read the whole file at its exact version.
How to install
mdr add fmschulz/omics-skills/bio-viromics@sha256:d6e197275de15765The 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_kwvsxdrqevof2t72)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 6 versions of this file, between Jul 12, 2026 and Oct 1, 2026, about one every 16 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20261001.bf5afd6 latest | 2026-10-01 | bf5afd6 | 9,118 B | A | view · diff |
| git:20260905.3e49039 | 2026-09-05 | 3e49039 | 7,540 B | A | view · diff |
| git:20260825.978bb0a | 2026-08-25 | 978bb0a | 7,361 B | A | view · diff |
| git:20260825.bd47e68 | 2026-08-25 | bd47e68 | 7,007 B | A | view · diff |
| git:20260713.88e759d | 2026-07-13 | 88e759d | 7,018 B | A | view · diff |
| git:20260712.3675171 | 2026-07-12 | 3675171 | 6,866 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 (9118 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_kwvsxdrqevof2t72 GET https://markdownregistry.com/api/v1/resolve?ref=fmschulz/omics-skills/bio-viromics GET https://markdownregistry.com/api/v1/blob/d6e197275de157657126bc9ca446e45cc3751a6d16e3c663f0fed96ab99192ad
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.