# Ena (npm · @pipeworx/mcp-ena)

European Nucleotide Archive (ENA) — EMBL-EBI's public record of raw sequencing runs, assemblies…

- Trust score: 81/100 (high trust)
- Change this week: +3
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-ena/ena-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-ena/ena-mcp)
- npm · `@pipeworx/mcp-ena`: 81/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena.md), [page](https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-ena`
- 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-ena).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 3 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 60/100
  - AI-judged instruction clarity (good).
  - Context-footprint check failed: tool/resource definitions use about 868 tokens (~289/item across 3 items; 3 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 3 captured tool definition(s), and no name or description among them implies an irreversible operation.
  - An AI judge read all 4 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 Ena MCP server?

Ena runs locally as an npm package, launched with npx -y @pipeworx/mcp-ena. 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-ena -- npx -y @pipeworx/mcp-ena
```

### Cursor

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

### VS Code

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

### Codex

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

### opencode

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

### OpenClaw

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

### Hermes

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

### Netclaw

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

### Vellum

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

### Other

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

## 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.

### 2026-11-03 (score 81, +1)

No change was recorded against any check on this day. Stability & Change Management went from 13 to 17. That category is still filling its 30-day observation window: 4 days of observed history at the previous scan, 5 at this one. The score rises as the window fills, whether or not the server changes.

### 2026-11-02 (score 80, +15)

- [security improvement] Malware scan: unverified → pass

### 2026-11-01 (score 65, −13)

- [security regression] Tool safety: pass → unverified
- [security regression] Malware scan: pass → unverified
- [security] Stability: Stability not yet verified: we do not have a sandbox capture of the MCP schema this version of the package serves yet.
- [functional regression] Tool coverage: 100 → unverified
- [functional regression] Capabilities: pass → unverified
- [functional improvement] Stability: unverified → 0.10
- [functional] First check of Schema quality: unverified
- [functional] Package version: 0.2.0 → 0.2.1

### 2026-10-30 (score 78, 0)

- [functional regression] Security disclosure: unverified → fail

### 2026-10-29 (score 78)

First indexed and scored.

## MCP tools (3)

### `ena_search` (~388 tokens)

Search the European Nucleotide Archive for sequencing runs, studies, samples, assemblies or annotated sequence using ENA's own query grammar. AUTHORITATIVE for "which public sequencing data exists for this organism / disease / country / platform" — ENA is an INSDC partner, so it covers data deposited to NCBI SRA and DDBJ as well. PREFER OVER WEB SEARCH for any question about what raw sequence data has been deposited. Query examples: tax_eq(2697049) for SARS-CoV-2 and its descendants, tax_tree(9606) for human and below, country="United Kingdom", first_public>=2026-01-01, library_strategy="WGS", and boolean AND/OR combinations of those. Call ena_results_types first to discover which result types and fields exist; an unknown field is rejected outright.

Input parameters:

- `fields` (string): Comma-separated columns to return. Omit for a sensible default set for the result type — an explicit empty value would return the accession column alone. Valid names per result type come from ena_res…
- `limit` (number): Maximum rows, 1-1000 (default 25). Note: upstream treats 0 as unlimited; this tool does not pass 0 through.
- `query` (string): ENA query expression, e.g. tax_eq(2697049), tax_tree(9606) AND library_strategy="WGS", country="Kenya" AND first_public>=2025-01-01. Omit to list the newest records of the result type.
- `result` (string): ENA result type to search. Common: read_run (raw sequencing runs), study, sample, experiment, analysis, assembly, sequence. Defaults to read_run. Full list from ena_results_types.
- `sortFields` (string): Comma-separated columns to sort by.

### `ena_filereport` (~284 tokens)

List every sequencing data file behind an ENA accession, with direct FASTQ/BAM/CRAM download URLs, byte sizes and MD5 checksums. AUTHORITATIVE for "where do I actually download the reads for this study/run/sample" — give it a study accession (PRJEB37886, PRJNA…), run (ERR…, SRR…, DRR…), sample (SAMEA…, SAMN…) or experiment, and it returns one row per run with its files. The multi-file semicolon-separated upstream fields are split into arrays here, so a caller does not silently fetch only the first mate of a paired-end run.

Input parameters:

- `accession` (string, required): ENA/INSDC accession: study (PRJEB37886, PRJNA…), run (ERR…/SRR…/DRR…), sample (SAMEA…/SAMN…), experiment (ERX…/SRX…) or taxon id. Must match the pattern the chosen result type accepts.
- `fields` (string): Comma-separated columns. Omit for a file-oriented default set (URLs, sizes, checksums).
- `limit` (number): Maximum rows, 1-1000 (default 25).
- `result` (string): Result type to report files for. Default read_run; also analysis, assembly, wgs_set.

### `ena_results_types` (~145 tokens)

List every ENA result type you can search — with its live record count and last-updated date — and, for one named result type, every field you may query or return. This is the schema-discovery step for ena_search: ENA rejects an unknown or wrong-result-type field name outright, so reading the field list first is cheaper than guessing. Also useful on its own for "how much public sequence data exists right now" — the counts are the archive's live totals.

Input parameters:

- `result` (string): Optional result type (e.g. read_run, study, sample) to also list its searchable/returnable fields. Omit to list result types only.

## Diagnostics

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

## Score history

- 2026-11-05: 81
- 2026-11-04: 81
- 2026-11-03: 81
- 2026-11-02: 80
- 2026-11-01: 65
- 2026-10-31: 78
- 2026-10-30: 78
- 2026-10-29: 78

## Common questions

### What is the Ena MCP server?

Ena is an MCP server listed in the public MCP registry as io.github.pipeworx-io/ena. European Nucleotide Archive (ENA), EMBL-EBI's public record of raw sequencing runs, assemblies… This page covers its npm package (@pipeworx/mcp-ena).

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

Ena scores 81 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 Ena MCP server expose?

Ena exposes 3 tools: ena_search, ena_filereport, ena_results_types. Their descriptions and schemas cost roughly 817 tokens of context every time the server is loaded.

### Is the Ena MCP server still maintained?

Ena 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 Ena MCP server under?

Ena 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 Ena MCP server?

VerifyMCP ran 16 checks on Ena, 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-ena
- Socket report: https://socket.dev/npm/package/@pipeworx/mcp-ena
- Repository: https://github.com/pipeworx-io/mcp-ena
- Website: https://pipeworx.io/packs/ena
- Changelog RSS feed: https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena.xml
- Changelog JSON feed: https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena/changelog.json
- Trust report (JSON): https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena.json
- HTML version of this page: https://verifymcp.io/servers/pipeworx-io-ena/pipeworx-mcp-ena