Ena
NPM · @PIPEWORX/MCP-ENA · 2 COMPONENTS
European Nucleotide Archive (ENA) — EMBL-EBI's public record of raw sequencing runs, assemblies…
Available components
Last scanned (16 hours ago)
Scores higher than 69% of npm servers
Category Health and Science
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. How we score → Why this is hard to score →
Supply Chain Security100
- No malware found by supply-chain analysis.Pass
- No known CVEs affecting this package version or its production dependencies.Pass
- No install/post-install scripts declared.Pass
- No production dependencies, so there is no dependency health to assess. View diagnostics → Pass
Provenance & Transparency97
- Source repository is publicly reachable at the declared URL. View diagnostics → Pass
- Cryptographically verified build provenance (signed, bound to pipeworx-io/mcp-ena). View diagnostics → Pass
- Clear OSI-approved license (MIT).Pass
- Actively maintained (last published 3 days ago).Pass
- Disclosure check failed: no security disclosure policy was found in the source repository. See how to fix → Fail
Schema Quality & AI Usability60
- AI-judged instruction clarity (good).Pass
- 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. See how to fix → Fail
- Usage-examples check failed: none of the tools include examples. See how to fix → Fail
Stability & Change Management23
- Stability observed for 7 of 30 days with no destabilising changes; credit accrues until the full window elapses.Partial
Tool Coverage100
- 100% of tools have a non-trivial description (not blank, and not just the tool's name).Pass
- 100% of tool parameters carry a description.Pass
Tool Safety100
- No prompt-injection markers were found in the server instructions, tool names or descriptions we captured.Pass
- We read all 3 captured tool definition(s), and no name or description among them implies an irreversible operation.Pass
- An AI judge read all 4 captured unit(s) of tool text and found none that tries to manipulate the model reading it.Pass
Capabilities100
- Implements a supported MCP spec version (2025-11-25); the latest is 2026-07-28.Pass
Checks we ran (16)
- Malware scan
- Known CVEs
- Install scripts
- Dependency health
- Source repository
- Provenance
- License
- Maintenance
- Security disclosure
- Schema quality
- Stability
- Tool coverage
- Injection markers
- Destructive annotations
- Judged manipulation
- MCP protocol
Does not apply to this package (2)
- Endpoint SecurityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
- Transport & ReachabilityScored on hosted endpoints only. A package has no live endpoint of its own for us to probe.
The score does not measure everything. What the score does not measure →
Every change we have recorded for this component, newest first. Security-relevant changes are always shown. ▲ marks a change for the better, ▼ a change for the worse; unmarked changes are neutral.
- 3 Nov 26 +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.
- 2 Nov 26 +15
- Malware scan: unverified → pass ▲ security
- 1 Nov 26 −13
- Tool safety: pass → unverified ▼ security
- 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. security
- Tool coverage: 100 → unverified ▼ functional
- Capabilities: pass → unverified ▼ functional
- Stability: unverified → 0.10 ▲ functional
- First check of Schema quality: unverified functional
- Package version: 0.2.0 → 0.2.1 functional
- 30 Oct 26 0
- Security disclosure: unverified → fail ▼ functional
- 29 Oct 26 78
First indexed and scored.
Diagnostic detail from the automated scan of this channel: what the scanner observed at each step, so you can see exactly where a check passed or failed. It is informational only and never changes the trust score.
Captured 5 Nov 2026 · Analysed npm/@pipeworx/mcp-ena@0.2.1
Provenance Verified
A signed build attestation was found and verified, binding this exact artifact to the source repository it claims to come from.
| Result | Verified |
|---|---|
| Ecosystem | npm |
| Reason | Verified |
| Discovered via | Registry attestation endpoint |
| Source repo | pipeworx-io/mcp-ena |
| Certificate issuer | https://token.actions.githubusercontent.com |
| Certificate SAN | https://github.com/pipeworx-io/mcp-ena/.github/workflows/publish.yml@refs/heads/main |
| Rekor log index | 3635919963 |
| Predicate type | SLSA build provenance https://slsa.dev/provenance/v1 |
| Subject digest | sha512:7dd7bdd92e5670dcbf5fb9e1a2b02cf37275074e6eb1ca97b790b88a13cd1115ba2e5b69d6a03349957dc41747067160ebaccbd1230d46aabe653618a |
Background: How many MCP packages publish verified provenance →
Dependencies 0 packages
| Packages resolved | 0 |
|---|---|
| Tree resolution | Complete |
Background: SBOMs and build attestations, explained →
The tools this component advertises to a client, with an estimated token cost for each. Expand a tool to see its parameters and schema. The per-tool counts are indicative and are not scored directly; the schema's total context footprint is one signal in Schema Quality & AI Usability. A tool's description is untrusted text the model reads on every call, which is what makes this list a security surface and not just an inventory: how tool poisoning works →
ena_filereport ~284
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.
| Name | Type | Req | Description |
|---|---|---|---|
| accession | string | yes | 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. |
No output schema declared.
No examples provided.
ena_results_types ~145
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.
| Name | Type | Req | Description |
|---|---|---|---|
| result | string | – | Optional result type (e.g. read_run, study, sample) to also list its searchable/returnable fields. Omit to list result types only. |
No output schema declared.
No examples provided.
ena_search ~388
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.
| Name | Type | Req | Description |
|---|---|---|---|
| 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. |
No output schema declared.
No examples provided.
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.
npm · @pipeworx/mcp-ena
claude mcp add pipeworx-io-ena -- npx -y @pipeworx/mcp-ena
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.