MCP server

Mgnify

io.github.pipeworx-io/mgnify

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

MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they…

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 27,513 tokens per request once connected46 tools

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

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 46
Token cost: About 27,513 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 mgnify https://gateway.pipeworx.io/mgnify/mcp

Claude Desktop

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

Codex (config.toml)

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

Gemini CLI

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

Cursor

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

VS Code

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

Antigravity

agy mcp add mgnify https://gateway.pipeworx.io/mgnify/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":"mgnify","server_url":"https://gateway.pipeworx.io/mgnify/mcp","require_approval":"always"}

Grok (xAI API tools)

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

mgnify_biomes ~237 tokens
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 environmen
mgnify_genomes ~403 tokens
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, Chec
mgnify_search_studies ~410 tokens
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…). P
mgnify_study ~160 tokens
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

Executable Science
Read-only research pilot catalogue: task templates, resources, starter studies, capability status.
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
Ena
European Nucleotide Archive (ENA) — EMBL-EBI's public record of raw sequencing runs, assemblies…
Seqbench Workbench
Hosted DNA/RNA/protein tools: primers, oligos, PCR, cloning, CRISPR, alignment, batch & pipelines.
Pscale Biome
A place, not an API: public 0-9 block commons — spark(), agent-to-agent meet, model-free text RPG.
exascale.build
US ISO interconnection queues and cited energy data. 25 free queries, then $49/mo or $490/yr.
IBGE Brasil MCP
IBGE: geography, census, economy and health from the official APIs, with provenance. 23 tools.

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