mcp-mgnifySAFE
MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they are classified under, and the ~57,000 MAGs and isolate genomes in its species-level genome catalogues, with completeness, contamination and GTDB taxonomy for each.
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
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.
Part of Pipeworx — an MCP gateway connecting AI agents to 1683+ live data sources.
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
- — study collection.
- — genome catalogues.
- — 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 "w
dedc73e3fa5dOBSERVED · 2026-10-11Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control.
claude mcp add mcp-mgnify -- npx -y @pipeworx/[email protected]
{
"mcpServers": {
"mcp-mgnify": {
"command": "npx",
"args": [
"-y",
"@pipeworx/[email protected]"
]
}
}
}Exposed tools (3)
3 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
mgnify_biomes | read | List MGnify\ |
mgnify_genomes | read | Search MGnify\ |
mgnify_search_studies | read | 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 |
Trust audit
SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | PASS |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- none-observed
- Network
- declared (1 observation(s))
- Shell
- none-observed
- Dependencies
- not all pinned
- Secrets in source
- none-found
Findings (1)
@modelcontextprotocol/sdk, tsx, typescript, @cloudflare/workers-types
Gates applied: no_behavioural_pass.
dedc73e3fa5dfull audit observations/trust-audit/mcp-server/pipeworx-io__mcp-mgnify.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-11 | dedc73e3fa5d | SAFE | B | 89 | first audit |
Questions
What is the mcp-mgnify MCP server?
MGnify — EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they are classified under, and the ~57,000 MAGs and isolate genomes in its species-level genome catalogues, with completeness, contamination and GTDB taxonomy for each.
What tools does mcp-mgnify expose?
3 in total: 3 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is mcp-mgnify safe to connect to an agent?
The audit found nothing in the source that contradicts what it says it does, and graded it B (89/100). Grade A is held back for packages that have also passed a sandboxed behavioural run, which is why a clean server reads B.
What credentials does mcp-mgnify need?
No credential environment variables were found in its source, so it appears to need none.
How does mcp-mgnify run?
It speaks stdio and streamable-http, so it runs as a local process your client starts. It is published on npm as @pipeworx/mcp-mgnify at 0.1.1.
How current is this page?
The grade is for one exact copy of the source (dedc73e3fa5d), read on 2026-10-11. The repository is watched and re-audited when it changes.