MGnify (EBI Metagenomics)

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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.

4tools
0msauth
free tier50 calls/day

Tools

mgnify_search_studies

Search MGnify for public metagenomics studies — the microbiome sequencing projects EMBL-EBI has assembled and annotated — by free text and/or biome lineage. AUTHORITATIVE for "what microbiome studies

No parameters required.

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mgnify_study

Fetch one MGnify metagenomics study in full by its accession (MGYS…) — title, controlled biome classification, the ENA project and study accessions behind it, available downloads and last-update date.

No parameters required.

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mgnify_genomes

Search MGnify's species-level genome catalogues — ~57,000 metagenome-assembled genomes (MAGs) and isolates from human gut, soil, marine, chicken and other biomes. AUTHORITATIVE for "is there a genome

No parameters required.

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mgnify_biomes

List MGnify's controlled biome vocabulary — the ~492 colon-delimited lineages (root:Host-associated:Human:Digestive system:Large intestine:Fecal, root:Environmental:Aquatic:Marine…) that every MGnify

No parameters required.

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Test with curl

The gateway speaks JSON-RPC 2.0 over HTTP POST. You can test any pack directly from the terminal.

List available tools
bash
curl -X POST https://gateway.pipeworx.io/mgnify/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/list"}'
Call a tool
bash
curl -X POST https://gateway.pipeworx.io/mgnify/mcp \
  -H "Content-Type: application/json" \
  -d '{"jsonrpc":"2.0","id":2,"method":"tools/call","params":{"name":"mgnify_search_studies","arguments":{}}}'

Use with the SDK

Install @pipeworx/sdk to call tools from any TypeScript/Node project.

TypeScript
import { Pipeworx } from '@pipeworx/sdk';
const px = new Pipeworx();
const result = await px.call("mgnify_search_studies", {});
ask_pipeworx
// Or ask in plain English:
const answer = await px.ask("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");