@pipeworx/mgnify

Connect: https://gateway.pipeworx.io/mgnify/mcp · Install: one-click buttons

No MCP client? Skip the connection: POST https://gateway.pipeworx.io/v1/tools/search_packs {"query":"..."} to find a tool below, GET /v1/tools/<name> for its schema, POST the same URL with arguments for the data — see For AI agents.

Tools: 4

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.

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.

Tools

• mgnify_search_studies — Search MGnify for public metagenomics studies — the microbiome sequencing projects EMBL-EBI has assembled and annotated — by free text and/or biome lineage. AUTHORITATIVE for “what microbiome studies
• mgnify_study — Fetch one MGnify metagenomics study in full by its accession (MGYS…) — title, controlled biome classification, the ENA project and study accessions behind it, available downloads and last-update date.
• mgnify_genomes — 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
• mgnify_biomes — List MGnify’s controlled biome vocabulary — the ~492 colon-delimited lineages (root:Host-associated:Human:Digestive system:Large intestine:Fecal, root:Environmental:Aquatic:Marine…) that every MGnify