Ena MCP Server

@pipeworx/ena

The European Nucleotide Archive (EMBL-EBI) — the public record of raw sequencing runs, assemblies and annotated sequence, searchable by organism, study, platform, collection country or date, with FASTQ/BAM download URLs and checksums for every run.

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

Tools

• ena_search(result?, query?, fields?, sortFields?, limit?) — search any ENA result type with ENA's own query grammar (tax_eq(2697049), tax_tree(9606) AND library_strategy="WGS", country="Kenya"). Answers "what public sequencing data exists for this organism / disease / place".
• ena_filereport(accession, result?, fields?, limit?) — every data file behind a study, run, sample or experiment accession, with direct download URLs, byte sizes and MD5s. Answers "where do I get the reads".
• ena_results_types(result?) — the schema-discovery step: every searchable result type with its live record count, and for one named type, every field it accepts. Call this before composing a query.

Auth

Keyless. No registration step.

Data sources

• https://www.ebi.ac.uk/ena/portal/api/search — typed search over result types.
• https://www.ebi.ac.uk/ena/portal/api/filereport — per-accession file listing.
• https://www.ebi.ac.uk/ena/portal/api/results — result types + live counts.
• https://www.ebi.ac.uk/ena/portal/api/returnFields — fields per result type.

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

• format=json is not the default. Without it you get TSV, which downstream reads as a single malformed string rather than as an error.
• limit=0 means UNLIMITED, the opposite of the usual convention. On read_run that is tens of millions of rows. This pack never sends 0.
• Numeric columns are strings on the wire ("read_count":"4547927").
• A search with no fields returns the accession column alone — a valid-looking, useless answer. The pack sends a default field set per result type.
• filereport rejects a mismatched accession with HTTP 200 and a {"message": ...} body naming the accepted regexes. We raise that message; returning an empty list would read as "this study has no runs".

Quick Start

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

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

What this endpoint actually serves

tools/list at https://gateway.pipeworx.io/ena/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/ena_search \
  -H 'Content-Type: application/json' \
  -d '{"result":"read_run","query":"tax_eq(2697049)","limit":3}'

No account needed for the first calls. Inspect any tool: GET https://gateway.pipeworx.io/v1/tools/ena_search. 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": {
    "ena": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-ena"]
    }
  }
}

Or run it directly to confirm it starts:

npx -y @pipeworx/mcp-ena

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 Ena data" })

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

More

• Docs and guides
• pipeworx.io

License

MIT