MCP server

Ucsc Genome

io.github.pipeworx-io/ucsc-genome

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

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

Website Source

At a glance

Type

MCP server

Publisher

pipeworx.io (verified by the MCP Registry)

Status

Working at last check

Tools

46

Token cost

About 28,279 tokens per request

Sets up in

Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok

Last checked

26 Oct 2026, 08:29 UTC

Connect it to your agent

Add to CursorAdd to VS CodeVS Code Insiders

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http ucsc-genome https://gateway.pipeworx.io/ucsc-genome/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.ucsc-genome]
url = "https://gateway.pipeworx.io/ucsc-genome/mcp"

Gemini CLI

{"mcpServers":{"ucsc-genome":{"httpUrl":"https://gateway.pipeworx.io/ucsc-genome/mcp"}}}

Cursor

{"mcpServers":{"ucsc-genome":{"url":"https://gateway.pipeworx.io/ucsc-genome/mcp"}}}

VS Code

{"servers":{"ucsc-genome":{"type":"http","url":"https://gateway.pipeworx.io/ucsc-genome/mcp"}}}

Antigravity

agy mcp add ucsc-genome https://gateway.pipeworx.io/ucsc-genome/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"ucsc-genome","server_url":"https://gateway.pipeworx.io/ucsc-genome/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"ucsc-genome","server_url":"https://gateway.pipeworx.io/ucsc-genome/mcp"}

Tools

• ucsc_genomes ~303 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 (hg3
• ucsc_sequence ~548 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 re
• ucsc_track_data ~682 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 (ge
• ucsc_tracks ~443 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,

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