# mcp-mgnify

> mcp-mgnify — pipeworx-io-mcp-mgnify. Use this tool when you need to access and analyze public microbiome studies, or retrieve information on metagenomics datasets, including genome catalogs and taxonomic classifications. It solves problems related to metagenomics research, such as identifying and characterizing microbial communities, and provides outputs including species-level genome catalogues and taxonomic information. It is ideal for use in bioinformatics and microbiology research contexts, accepting inputs such as genome sequences and biome vocabulary terms.

Canonical page: https://skillsregistry.net/skills/pipeworx-io-mcp-mgnify  
JSON: https://api.skillsregistry.net/v1/skills/pipeworx-io-mcp-mgnify

## Description

MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they are classified under, and the ~57,000 MAGs and isolate genomes in its species-level genome catalogues, with completeness, contamination and GTDB taxonomy for each.

## Trust

- **Trust score (0–1):** 0.97
- **Verification tier:** verified
- **Last scanned:** 2026-09-28

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** container
- **Runtime environment:** vm
- **License:** MIT
- **Updated:** 2026-09-28

## Source

- **Source listing:** [GitHub](https://github.com/pipeworx-io/mcp-mgnify)

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "pipeworx-io-mcp-mgnify"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/pipeworx-io-mcp-mgnify` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/pipeworx-io-mcp-mgnify/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt