ENCODE Toolkit — Claude Code MCP server: what it does, how to install
Twenty tools and 47 skills over the ENCODE Project: find experiments, pull data, run analysis pipelines and cross-reference other genomics databases.
claude mcp add encode-toolkit -- npx -y encode-toolkitWhat ENCODE Toolkit does
The server connects your agent to the live ENCODE API. Ask for histone ChIP-seq in a given tissue, get the experiments, download the files, then run one of the bundled pipelines. Skills cover the neighbouring resources too: GTEx expression, ClinVar significance, GWAS Catalog associations, gnomAD frequencies, Ensembl annotation, UCSC tracks and JASPAR motifs.
Nothing to authenticate against — these are public databases. You do need Node.js, because the server starts through npx -y encode-toolkit.
The release is marked beta at 0.3.4. Fine for exploratory work; if results feed a paper, test your own queries on known data first. Licensing is AGPL-3.0, so shipping it inside a hosted product carries copyleft obligations.
What it helps with
- locate ChIP-seq experiments by tissue and target
- download ENCODE files without sorting formats by hand
- check variant significance against ClinVar
- line up peaks with GWAS Catalog positions
- draft a methods section with source references
Example prompts for the agent
- Find every histone ChIP-seq experiment for human pancreas tissue
- Download the peaks for that experiment and list nearby genes
- Cross-check these variants in ClinVar and gnomAD, then build a table
How to install ENCODE Toolkit
Platform CLI
claude mcp add encode-toolkit -- npx -y encode-toolkitPlatform CLI
codex mcp add encode-toolkit -- npx -y encode-toolkitConfig file
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}Config file
{
"servers": {
"encode-toolkit": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"encode-toolkit"
]
}
}
}Platform CLI
gemini mcp add encode-toolkit npx -y encode-toolkitStep by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about ENCODE Toolkit
How do I install ENCODE Toolkit in Claude Code?
Run claude mcp add encode-toolkit -- npx -y encode-toolkit, then restart the session. No API key is involved.
What does ENCODE Toolkit do?
It gives the agent 20 ENCODE API tools plus 47 skills for related databases. Search, download, pipelines and a methods draft all happen in one conversation.
Which platforms are supported?
Claude, Codex, Cursor, GitHub Copilot, Windsurf, Cline and Zed. Cursor and Copilot take the server through their MCP settings file.
