Mgnify MCP Server

@pipeworx/mgnify

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

Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.

Tools

• mgnify_search_studies(search?, biome_lineage?, limit?) — microbiome studies by free text and/or biome, each with its ENA project accessions.
• mgnify_study(accession) — one MGYS study in full.
• mgnify_genomes(search?, catalogue_id?, taxon_lineage?, limit?) — the genome catalogues, with CheckM completeness/contamination, N50, GC, origin and ENA/NCBI cross-references.
• mgnify_biomes(lineage_prefix?, limit?) — the ~492-lineage biome vocabulary. The exact lineage strings are not guessable; look them up here first.

Auth

Keyless. No registration step.

Data sources

• https://www.ebi.ac.uk/metagenomics/api/v2/studies/ — study collection.
• https://www.ebi.ac.uk/metagenomics/api/v2/genomes/ — genome catalogues.
• https://www.ebi.ac.uk/metagenomics/api/v2/biomes/ — biome vocabulary.

Things that cost time to rediscover (measured 2026-09-17)

• This pack targets v2 deliberately. v1 is still up and still serves a study list, but GET /v1/studies/MGYS00010519 returns Not found for a study v2 serves in full. A v1-based pack would answer "that study does not exist" about studies that do.
• Most query filters are silently ignored. catalogue_id=, taxon_lineage=, biome_name= and lineage= all return the FULL unfiltered collection — same count, same first row, no error. Only search= narrows anything (studies 5,684 → 532 for "gut"; genomes 56,782 → 787 for "Prevotella"). This pack passes search through and applies the rest client-side, reporting rows_scanned and scan_exhausted so a caller can tell "no matches" from "we stopped looking".
• search= does not work on /biomes either. The 492-row vocabulary comes back whole whatever you ask, so mgnify_biomes pages it and filters here.
• Collection URLs need a trailing slash (/v2/studies/?…; without it, 301). Detail URLs must NOT have one (/v2/studies/MGYS00010519).
• page_size caps at 100 and clamps silently — asking for 500 returns 100 with no indication the request was reduced.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

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

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/mgnify/mcp returns the tools in the table above plus the shared Pipeworx meta-tools — ask_pipeworx, discover_tools, search_within, remember/recall and the rest of the gateway-wide set. So the tool count you see is larger than this table: a single-pack endpoint currently lists roughly 30 shared tools alongside the pack's own. The connection's initialize response states its exact scope, and is the authoritative answer for a given day.

This is deliberate, not multiplexing by accident. The meta-tools are what let a scoped connection answer a question this pack does not cover — via ask_pipeworx, which routes across the whole catalog — without you adding a second MCP server. There is currently no way to mount a pack endpoint without them; if the extra schemas cost you more context than the routing is worth, connect to the full gateway once rather than to several pack endpoints.

Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:

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

Both URLs reach the same gateway and the same 1683+ data sources. The only difference is which pack's tools are listed directly; ask_pipeworx reaches all of them from either one.

No MCP client? Call it over HTTP

curl -X POST https://gateway.pipeworx.io/v1/tools/mgnify_search_studies \
  -H 'Content-Type: application/json' \
  -d '{"search":"gut","limit":3}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/mgnify_search_studies. Find one: POST https://gateway.pipeworx.io/v1/tools/search_packs with {"query":"..."}.

Standalone (no gateway account)

This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:

{
  "mcpServers": {
    "mgnify": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-mgnify"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-mgnify

It speaks MCP over stdin/stdout and answers initialize/tools/list/tools/call for only this pack's tools — none of the shared meta-tools the gateway connection above adds. Same source, same tools, no ask_pipeworx routing.

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:

ask_pipeworx({ question: "your question about Mgnify data" })

The gateway picks the right tool and fills the arguments automatically.

More

• Docs and guides
• pipeworx.io

License

MIT