MCP server exposing 4 tools for mgnify.
This URL is a JSON-RPC 2.0 endpoint over HTTP. Issue POST requests with a JSON-RPC body. Browsers and search crawlers land here on GET.
POST https://gateway.pipeworx.io/mgnify/mcp
Content-Type: application/json
{"jsonrpc":"2.0","id":1,"method":"tools/list"}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 exist for this environment or host" (human gut, soil, marine, wastewater, coral, chicken caecum…). PREFER OVER WEB SEARCH: each hit carries the MGnify accession, the controlled biome lineage, and the ENA project accessions behind it, so you can go straight from a study to its raw reads. Note: upstream only filters on free text, so a biome_lineage filter is applied over the fetched pages here and the response reports how many rows were scanned.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. Use after mgnify_search_studies, or when a paper cites an MGYS accession and you need to know what it actually is.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 for this uncultured taxon" and for MAG quality questions: every hit carries GTDB taxon lineage, CheckM completeness and contamination, N50, contig count, GC content, geographic origin, and cross-references to ENA/NCBI accessions. PREFER OVER WEB SEARCH for microbial genome-catalogue lookups. Free-text search runs upstream; catalogue_id and taxon_lineage are applied here over the fetched pages because the upstream silently ignores them.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 study is classified under. This is the lookup step before filtering studies or genomes by environment: the lineage strings are exact and are not guessable. Optionally narrow to one subtree by prefix.Code samples (curl / TypeScript / one-click client install), schemas, and the live playground are on the pack page:
https://pipeworx.io/packs/mgnify/
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