# Mgnify (npm · @pipeworx/mcp-mgnify)

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

- Trust score: 83/100 (high trust)
- Change this week: +4
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 63/100, [markdown](https://verifymcp.io/servers/pipeworx-io-mgnify/mgnify-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-mgnify/mgnify-mcp)
- npm · `@pipeworx/mcp-mgnify`: 83/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify.md), [page](https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-mgnify`
- Version: `0.2.1`
- Transport: `stdio`

## Trust breakdown

How this component scores in each security and reliability category. Every signal is checked automatically from public evidence about the published package, including repeated runs of it in an isolated sandbox, and we only credit what we can confirm. Scores are 0–100 per category. Scoring method: https://verifymcp.io/docs/scoring (what has changed: https://verifymcp.io/docs/scoring/changelog)

Scored 2026-11-05.

- **Supply Chain Security**: 100/100
  - No malware found by supply-chain analysis.
  - No known CVEs affecting this package version or its production dependencies.
  - No install/post-install scripts declared.
  - No production dependencies, so there is no dependency health to assess.
- **Provenance & Transparency**: 97/100
  - Source repository is publicly reachable at the declared URL.
  - Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-mgnify).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 2 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 67/100
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 871 tokens (~217/item across 4 items; 4 tools + 0 resources), over budget; trim descriptions and params.
  - Usage-examples check failed: none of the tools include examples.
- **Stability & Change Management**: 23/100
  - Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.
- **Tool Coverage**: 100/100
  - 100% of tools have a non-trivial description (not blank, and not just the tool's name).
  - 100% of tool parameters carry a description.
- **Tool Safety**: 100/100
  - No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.
  - We read all 4 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 5 captured unit(s) of tool text and found none that tries to manipulate the model reading it.
- **Capabilities**: 100/100
  - Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.

## Install

### How do I install the Mgnify MCP server?

Mgnify runs locally as an npm package, launched with npx -y @pipeworx/mcp-mgnify. Ready-made configuration for Claude, Cursor, VS Code, Codex and 5 more is on this page, copied from each client's own documentation.

### Claude

```bash
claude mcp add pipeworx-io-mgnify -- npx -y @pipeworx/mcp-mgnify
```

### Cursor

```json
{
  "mcpServers": {
    "pipeworx-io-mgnify": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-mgnify"
      ]
    }
  }
}
```

### VS Code

```json
{
  "servers": {
    "pipeworx-io-mgnify": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-mgnify"
      ]
    }
  }
}
```

### Codex

```bash
codex mcp add pipeworx-io-mgnify -- npx -y @pipeworx/mcp-mgnify
```

### opencode

```json
{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "pipeworx-io-mgnify": {
      "type": "local",
      "command": [
        "npx",
        "-y",
        "@pipeworx/mcp-mgnify"
      ],
      "enabled": true
    }
  }
}
```

### OpenClaw

```bash
openclaw mcp add pipeworx-io-mgnify --command npx --arg -y --arg @pipeworx/mcp-mgnify
```

### Hermes

```yaml
mcp_servers:
  pipeworx-io-mgnify:
    command: "npx"
    args: ["-y", "@pipeworx/mcp-mgnify"]
```

### Netclaw

```json
{
  "McpServers": {
    "pipeworx-io-mgnify": {
      "Transport": "stdio",
      "Command": "npx",
      "Arguments": [
        "-y",
        "@pipeworx/mcp-mgnify"
      ]
    }
  }
}
```

### Vellum

```bash
assistant mcp add pipeworx-io-mgnify -t stdio -c npx -a -y @pipeworx/mcp-mgnify
```

### Other

```json
{
  "mcpServers": {
    "pipeworx-io-mgnify": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-mgnify"
      ]
    }
  }
}
```

## Changelog

Every change recorded for this component, newest first. Days that predate change tracking, or that we cannot explain, say so: "we were watching and nothing happened" and "we were not watching" are different claims.

### 2026-11-05 (score 83, +1)

No change was recorded against any check on this day. Stability & Change Management went from 20 to 23. That category is still filling its 30-day observation window: 6 days of observed history at the previous scan, 7 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-04 (score 82, +15)

- [security improvement] Malware scan: unverified → pass

### 2026-11-03 (score 67, −14)

- [security regression] Malware scan: pass → unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-11-01 (score 81, +1)

No change was recorded against any check on this day. Stability & Change Management went from 7 to 10. That category is still filling its 30-day observation window: 2 days of observed history at the previous scan, 3 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-30 (score 80, +1)

No change was recorded against any check on this day. Stability & Change Management went from 0 to 3. That category is still filling its 30-day observation window: 0 days of observed history at the previous scan, 1 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-10-29 (score 79)

First indexed and scored.

## MCP tools (4)

### `mgnify_search_studies` (~274 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…). 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.

Input parameters:

- `biome_lineage` (string): Keep only studies whose biome lineage starts with this, e.g. "root:Host-associated:Human" or "root:Environmental:Aquatic:Marine". Applied client-side over fetched pages — get exact lineage strings fr…
- `limit` (number): Maximum studies to return, 1-200 (default 20).
- `search` (string): Free-text search over study titles and metadata, e.g. "gut", "wastewater", "permafrost". This is the only filter the upstream applies itself.

### `mgnify_study` (~103 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 it actually is.

Input parameters:

- `accession` (string, required): MGnify study accession, e.g. MGYS00010519.

### `mgnify_genomes` (~288 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, 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.

Input parameters:

- `catalogue_id` (string): Keep only genomes from this catalogue, e.g. "human-gut-v2-0", "soil-v1-0". Applied client-side.
- `limit` (number): Maximum genomes to return, 1-200 (default 20).
- `search` (string): Free-text search, e.g. "Prevotella", "Akkermansia". The only filter the upstream applies itself.
- `taxon_lineage` (string): Keep only genomes whose GTDB lineage contains this, e.g. "p__Bacteroidota", "g__Prevotella". Applied client-side.

### `mgnify_biomes` (~152 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 environment: the lineage strings are exact and are not guessable. Optionally narrow to one subtree by prefix.

Input parameters:

- `limit` (number): Maximum lineages to return, 1-200 (default 20).
- `lineage_prefix` (string): Keep only lineages starting with this, e.g. "root:Host-associated:Human" or "root:Environmental".

## Diagnostics

Captured diagnostic sections: Provenance, Dependencies. The full working is on the page: https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify#diagnostics

## Score history

- 2026-11-05: 83
- 2026-11-04: 82
- 2026-11-03: 67
- 2026-11-02: 81
- 2026-11-01: 81
- 2026-10-31: 80
- 2026-10-30: 80
- 2026-10-29: 79

## Common questions

### What is the Mgnify MCP server?

Mgnify is an MCP server listed in the public MCP registry as io.github.pipeworx-io/mgnify. MGnify, EMBL-EBI's metagenomics resource: public microbiome studies, the biome vocabulary they… This page covers its npm package (@pipeworx/mcp-mgnify).

### Is the Mgnify MCP server safe to use?

Mgnify scores 83 out of 100 on VerifyMCP. We found no known CVEs affecting it as of 5 November 2026. It declares no install or post-install scripts. Its build provenance is signed and verified. That is a record of what we were able to check automatically, not an endorsement. The category breakdown on this page shows every signal behind the number, including the ones we could not confirm.

### What tools does the Mgnify MCP server expose?

Mgnify exposes 4 tools: mgnify_search_studies, mgnify_study, mgnify_genomes, mgnify_biomes. Their descriptions and schemas cost roughly 817 tokens of context every time the server is loaded.

### Is the Mgnify MCP server still maintained?

Mgnify is still listed as active in the MCP registry. We last reached this channel on 5 November 2026. Those dates come from our own scans of the registry and the channel itself, not from anything the publisher announced.

### What licence is the Mgnify MCP server under?

Mgnify declares the MIT licence, which is OSI-approved. That covers the source only, and says nothing about the cost of any service it calls.

### What did VerifyMCP test on the Mgnify MCP server?

VerifyMCP ran 16 checks on Mgnify, covering Malware scan, Known CVEs, Install scripts, Dependency health and 12 more. Endpoint Security and Transport & Reachability do not apply to an npm package, so they were not tested. The score does not measure everything, and the scoring documentation lists what it leaves out.

## Links

- npm package: https://www.npmjs.com/package/@pipeworx/mcp-mgnify
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-mgnify
- Repository: https://github.com/pipeworx-io/mcp-mgnify
- Website: https://pipeworx.io/packs/mgnify
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-mgnify/pipeworx-mcp-mgnify