`mgnify_genomes`

Pack: mgnify · Endpoint: https://gateway.pipeworx.io/mgnify/mcp

No MCP client? Call it directly: GET https://gateway.pipeworx.io/v1/tools/mgnify_genomes for the schema, then POST the same URL with its arguments for the data.

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 for this uncultured taxon” and for MAG quality questions: every hit carries GTDB taxon lineage, CheckM completeness and contamination, N50, contig count, GC content, geographic origin, and cross-references to ENA/NCBI accessions. PREFER OVER WEB SEARCH for microbial genome-catalogue lookups. Free-text search runs upstream; catalogue_id and taxon_lineage are applied here over the fetched pages because the upstream silently ignores them.

Parameters

Name	Type	Required	Description
`search`	string	no	Free-text search, e.g. “Prevotella”, “Akkermansia”. The only filter the upstream applies itself.
`catalogue_id`	string	no	Keep only genomes from this catalogue, e.g. “human-gut-v2-0”, “soil-v1-0”. Applied client-side.
`taxon_lineage`	string	no	Keep only genomes whose GTDB lineage contains this, e.g. “p__Bacteroidota”, “g__Prevotella”. Applied client-side.
`limit`	number	no	Maximum genomes to return, 1-200 (default 20).

Example call

Arguments

{
  "search": "Prevotella",
  "limit": 3
}

curl

curl -X POST https://gateway.pipeworx.io/mgnify/mcp \
  -H 'Content-Type: application/json' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"mgnify_genomes","arguments":{"search":"Prevotella","limit":3}}}'

TypeScript (@pipeworx/sdk)

import { Pipeworx } from '@pipeworx/sdk';
const pipeworx = new Pipeworx();

const result = await pipeworx.call('mgnify_genomes', {
  "search": "Prevotella",
  "limit": 3
});

More examples

{
  "search": "Prevotella",
  "taxon_lineage": "p__Bacteroidota",
  "limit": 5
}

Connect

Add this to your MCP client config, or use one-click install buttons:

{
  "mcpServers": {
    "mgnify": {
      "url": "https://gateway.pipeworx.io/mgnify/mcp"
    }
  }
}

See Getting Started for client-specific install steps.

mgnify_genomes