MCP server

Ena

io.github.pipeworx-io/ena

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

European Nucleotide Archive (ENA) — EMBL-EBI's public record of raw sequencing runs, assemblies…

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 27,476 tokens per request once connected45 tools

https://gateway.pipeworx.io/ena/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 45
Token cost: About 27,476 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http ena https://gateway.pipeworx.io/ena/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.ena]
url = "https://gateway.pipeworx.io/ena/mcp"

Gemini CLI

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

Cursor

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

VS Code

{"servers":{"ena":{"type":"http","url":"https://gateway.pipeworx.io/ena/mcp"}}}

Antigravity

agy mcp add ena https://gateway.pipeworx.io/ena/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"ena","server_url":"https://gateway.pipeworx.io/ena/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"ena","server_url":"https://gateway.pipeworx.io/ena/mcp"}

ena_filereport ~396 tokens
List every sequencing data file behind an ENA accession, with direct FASTQ/BAM/CRAM download URLs, byte sizes and MD5 checksums. AUTHORITATIVE for "where do I actually download the reads for this study/run/sample" — give it a study accession (PRJEB37886, PRJNA…), run (ERR…, SRR…, DRR…), sample (SAME
ena_results_types ~222 tokens
List every ENA result type you can search — with its live record count and last-updated date — and, for one named result type, every field you may query or return. This is the schema-discovery step for ena_search: ENA rejects an unknown or wrong-result-type field name outright, so reading the field
ena_search ~555 tokens
Search the European Nucleotide Archive for sequencing runs, studies, samples, assemblies or annotated sequence using ENA's own query grammar. AUTHORITATIVE for "which public sequencing data exists for this organism / disease / country / platform" — ENA is an INSDC partner, so it covers data deposite

Mgnify
MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they…
Ncbi Datasets
NCBI Datasets — the US National Library of Medicine's genome, gene and taxonomy reference service…
Seqbench Workbench
Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
AgentBazaar: Beyond Obvious
Answers past the generic one, A2A agent invoke, and free public Data APIs as compact rows.
SiteCheck Health & Travel
121 pay-per-call agent tools: health care, drug, provider and travel data tools. x402
Jean — Molecular Biology & Genomics
Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics
IARCCUM Archive of Anglican-Roman Catholic Dialogue
Read-only access to public records on Anglican-Roman Catholic dialogue in the IARCCUM Archive.
MachineWitness
EU archive of the machine-readable web: check a domain, order a time-stamped record or extract.

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