ocean-genomics SKILL.md skillA
ocean-genomics from broomva/skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add broomva/skills/ocean-genomics@git:20260721.2758b4cPins git:20260721.2758b4c in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- broomva/skills
- Path
skills/science/ocean-genomics/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260721.2758b4c, committed Jul 21, 2026
- First version recorded
- Jun 28, 2026
- Size
- 11,812 bytes
- Repository stars
- 5
- License
- MIT
Comprehensive bioinformatics and ocean genomics skill for eDNA metabarcoding, metagenomics, protein structure prediction, and marine biodiversity analysis. Use when: (1) Working with DNA/RNA sequences (FASTQ, FASTA, SAM/BAM, VCF files), (2) Running BLAST, QIIME2, Kraken2, or Nextflow pipelines, (3) Predicting protein structures via ESMFold2, AlphaFold, or ColabFold, (4) Analyzing environmental DNA (eDNA) from marine samples, (5) Querying marine databases (OBIS, BOLD, DOO, GenBank, UniProt)…
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
# Ocean Genomics
Agentic bioinformatics skill for ocean genomics — from eDNA water sampling to species identification, protein structure prediction, and scientific insight publication.
## Quick Start
### 1. Set Up MCP Integration
Install gget-MCP for immediate access to BLAST, AlphaFold, sequence retrieval, and 9 other genomics tools:
```json
// Add to .claude/settings.json → mcpServers
{
"gget-mcp": {
"command": "uvx",
"args": ["--from", "gget-mcp@latest", "stdio"]
}
}
```
### 2. Install CLI Tools
```bash
# Core tools
brew install blast mmseqs2 samtools minimap2 nextflow
pip install biopython biotite gget
# Nanopore basecalling (runs on Apple Silicon)
brew install nanoporetech/dorado/dorado
# eDNA pipeline (conda recommended)
conda create -n edna -c bioconda -c conda-forge qiime2 kraken2 fastp fastqc
```
### 3. Install Companion Skills
```bash
npx skills add adaptyvbio/protein-design-skills@alphafold -g -y
npx skills add anthropics/life-sciences@nextflow-development -g -y
npx skills add gptomics/bioskills@bioskills -g -y
npx skills add davila7/claude-code-templates@gget -g -y
```
## Core Workflows
### Workflow A: eDNA Species Inventory
…Read the whole file at its exact version.
How to install
mdr add broomva/skills/ocean-genomics@sha256:1c8647b65a6b56f4The line at the top of this page pins the label git:20260721.2758b4c, 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_f3365hc36sgv4xt7)
5 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Jun 28, 2026 and Jul 21, 2026, about one every 24 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260721.2758b4c latest | 2026-07-21 | 2758b4c | 11,812 B | A | view · diff |
| git:20260628.9edbf07 | 2026-06-28 | 9edbf07 | 10,170 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 (11812 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
broomva/skills · 5 stars · license MIT · pushed 2026-11-07 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_f3365hc36sgv4xt7 GET https://markdownregistry.com/api/v1/resolve?ref=broomva/skills/ocean-genomics GET https://markdownregistry.com/api/v1/blob/1c8647b65a6b56f42101c593bcc897f90e44240a9aa59be6827b6e4f4acfd985
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.