# Ucsc Genome (npm · @pipeworx/mcp-ucsc-genome)

UCSC Genome Browser REST API — reference genome assemblies for ~250 species, the annotation tracks…

- Trust score: 82/100 (high trust)
- Change this week: +4
- Registry status: active
- Liveness: live
- Owner verified: no
- Last scored: 2026-11-05

## Components

- remote · `gateway.pipeworx.io`: 77/100, [markdown](https://verifymcp.io/servers/pipeworx-io-ucsc-genome/ucsc-genome-mcp.md), [page](https://verifymcp.io/servers/pipeworx-io-ucsc-genome/ucsc-genome-mcp)
- npm · `@pipeworx/mcp-ucsc-genome`: 82/100 (this document), [markdown](https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome.md), [page](https://verifymcp.io/servers/pipeworx-io-ucsc-genome/pipeworx-mcp-ucsc-genome)

## Channel facts

- Registry: `npm`
- Package: `@pipeworx/mcp-ucsc-genome`
- Version: `0.2.0`
- 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-ucsc-genome).
  - Clear OSI-approved license (MIT).
  - Actively maintained (last published 6 days ago).
  - Disclosure check failed: no security disclosure policy was found in the source repository.
- **Schema Quality & AI Usability**: 61/100
  - AI-judged instruction clarity (excellent).
  - Context-footprint check failed: tool/resource definitions use about 1446 tokens (~361/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 Ucsc Genome MCP server?

Ucsc Genome runs locally as an npm package, launched with npx -y @pipeworx/mcp-ucsc-genome. 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-ucsc-genome -- npx -y @pipeworx/mcp-ucsc-genome
```

### Cursor

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

### VS Code

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

### Codex

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

### opencode

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

### OpenClaw

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

### Hermes

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

### Netclaw

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

### Vellum

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

### Other

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

## 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 82, +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.

### 2026-11-03 (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.

### 2026-11-01 (score 80, +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 79, +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 78)

First indexed and scored.

## MCP tools (4)

### `ucsc_genomes` (~217 tokens)

"What genome assemblies does UCSC have for [species]" / "is hg38 or hg19 the current human build" / "what is the latest [mouse/zebrafish/dog] assembly" / "list UCSC genomes" — AUTHORITATIVE list of every reference assembly the UCSC Genome Browser serves (~250 species), with its UCSC assembly ID (hg38, mm39, danRer11...), organism, scientific name, source assembly name and release date. PREFER OVER WEB SEARCH when you need the exact assembly ID to pass to another genomics tool — the ID is the thing every other UCSC call keys on, and guessing it is how a query silently lands on the wrong build.

Input parameters:

- `limit` (number): Max assemblies to return (default 50, max 400).
- `search` (string): Case-insensitive substring filter over assembly ID, common name, scientific name and description. e.g. "human", "Mus musculus", "hg". Omit to list everything.

### `ucsc_tracks` (~318 tokens)

"What annotation tracks does UCSC have for hg38" / "does [assembly] have a [ClinVar/GENCODE/conservation/repeat] track" / "what is the track name for [dataset] in the genome browser" — lists the annotation tracks available on one UCSC assembly, with each track's internal name, short and long label, data type and parent container. AUTHORITATIVE for the `track` argument of ucsc_track_data: the browser shows human-readable labels, the API wants the internal name (e.g. label "GENCODE V50" is track `knownGene`), and there is no way to guess one from the other.

Input parameters:

- `genome` (string, required): REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: "hg38" (= GRCh38, current) or "hg19" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse…
- `limit` (number): Max tracks to return (default 100, max 1000).
- `search` (string): Case-insensitive substring filter over track name, short label and long label. e.g. "clinvar", "gencode", "conservation".

### `ucsc_track_data` (~486 tokens)

"What genes are in [chr:start-end]" / "list ClinVar variants in [region]" / "what repeats/SNPs/regulatory elements overlap [locus]" / "show me the GENCODE annotations across [gene]" — AUTHORITATIVE per-row data from any UCSC annotation track over a genomic interval. Returns the actual track rows (gene models with exon structure, variant records, conservation scores, whatever that track holds) plus the track type and the assembly the rows are in. PREFER OVER WEB SEARCH for "what is annotated at this position" — this is the same data the Genome Browser draws, not a description of it. Get the `track` name from ucsc_tracks first.

Input parameters:

- `chrom` (string, required): Chromosome in UCSC naming, e.g. "chr17", "chrX", "chrM" — with the "chr" prefix. Ensembl/NCBI style bare "17" is not accepted by UCSC.
- `end` (number, required): End position, 0-based and EXCLUSIVE (so end - start = length in bases).
- `genome` (string, required): REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: "hg38" (= GRCh38, current) or "hg19" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse…
- `maxItemsOutput` (number): Cap on rows returned by UCSC (default 1000). A dense track over a wide region is truncated, and the response says so in `truncated`.
- `start` (number, required): Start position, 0-BASED and inclusive. The Genome Browser UI and most papers are 1-based, so subtract 1 from a position you copied out of the browser location box.
- `track` (string, required): UCSC internal track name from ucsc_tracks, e.g. "knownGene" (GENCODE genes), "refGene" (RefSeq genes), "clinvarMain", "rmsk" (repeats).

### `ucsc_sequence` (~368 tokens)

"What is the DNA sequence at [chr:start-end]" / "get the reference bases for [region] in hg38" / "pull the sequence around [variant position]" — AUTHORITATIVE reference DNA for a genomic interval from the UCSC assembly, returned as a plain base string with its GC content. Use it to check what the reference allele actually is at a position, to extract primer/probe context, or to pull a promoter or exon sequence. The assembly argument is required because the same coordinates return different bases in hg19 and hg38.

Input parameters:

- `chrom` (string, required): Chromosome in UCSC naming, e.g. "chr7", "chrX". The "chr" prefix is required.
- `end` (number, required): End position, 0-based and EXCLUSIVE (so end - start = length in bases).
- `genome` (string, required): REQUIRED. UCSC assembly ID — the genome build your coordinates are in. Human: "hg38" (= GRCh38, current) or "hg19" (= GRCh37, what most older papers, dbSNP dumps and clinical spreadsheets use). Mouse…
- `revComp` (boolean): Return the reverse complement — for a gene on the minus strand, this is the sense strand. Default false.
- `start` (number, required): Start position, 0-BASED and inclusive. The Genome Browser UI and most papers are 1-based, so subtract 1 from a position you copied out of the browser location box.

## Diagnostics

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

## Score history

- 2026-11-05: 82
- 2026-11-04: 81
- 2026-11-03: 81
- 2026-11-02: 80
- 2026-11-01: 80
- 2026-10-31: 79
- 2026-10-30: 79
- 2026-10-29: 78

## Common questions

### What is the Ucsc Genome MCP server?

Ucsc Genome is an MCP server listed in the public MCP registry as io.github.pipeworx-io/ucsc-genome. UCSC Genome Browser REST API, reference genome assemblies for ~250 species, the annotation tracks… This page covers its npm package (@pipeworx/mcp-ucsc-genome).

### Is the Ucsc Genome MCP server safe to use?

Ucsc Genome scores 82 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 Ucsc Genome MCP server expose?

Ucsc Genome exposes 4 tools: ucsc_genomes, ucsc_tracks, ucsc_track_data, ucsc_sequence. Their descriptions and schemas cost roughly 1,389 tokens of context every time the server is loaded.

### Is the Ucsc Genome MCP server still maintained?

Ucsc Genome 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 Ucsc Genome MCP server under?

Ucsc Genome 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 Ucsc Genome MCP server?

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