The full upstream README, mirrored here for reference. Install config, tool schemas, adoption signals, and an original overview live on the Ena listing page.
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.
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.Keyless. No registration step.
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."read_count":"4547927").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".Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
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:
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 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":"..."}.
This package also runs as a local stdio MCP server — no Pipeworx account, no gateway round-trip:
Or run it directly to confirm it starts:
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.
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:
The gateway picks the right tool and fills the arguments automatically.
MIT