Genomics Research Infrastructure for Claude
ENCODE Toolkit — Genomics Research Infrastructure for Claude
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
Start from ENCODE but go everywhere: discover histone peaks, cross-reference with GWAS variants, check ClinVar pathogenicity, pull GTEx expression, analyze TF binding motifs from JASPAR, run pipelines, and generate publication-ready methods with full provenance — in one conversation.
Citation Notes
If you use ENCODE-Toolkit, please cite:
Alex M. Mawla. (2026). ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis. Zenodo. https://doi.org/10.5281/zenodo.18917511
BibTeX
@software{mawla_2026_encode_toolkit,
author = {Mawla, Alex M.},
title = {ENCODE-Toolkit: an MCP server, Claude plugin, and skills suite for ENCODE genomic data access and analysis},
year = {2026},
publisher = {Zenodo},
doi = {10.5281/zenodo.18917511},
url = {https://doi.org/10.5281/zenodo.18917511}
}
Quick Start
Claude Code Plugin (recommended)
Start a new Claude Code session and enter:
/plugin marketplace add ammawla/encode-toolkit
/plugin install encode-toolkit
That's it. All 20 tools, 47 skills, and the MCP connector are now available.
MCP-only install (tools only, no skills)
If you only need the 20 MCP tools without the 47 workflow skills:
claude mcp add encode -- uvx encode-toolkit
Other editors and platforms
npx (Node.js)
npx encode-toolkit
Or in MCP client config: { "command": "npx", "args": ["encode-toolkit"] }
pip install
pip install encode-toolkit
Then use encode-toolkit as the command in any MCP client configuration:
{
"mcpServers": {
"encode": {
"command": "encode-toolkit"
}
}
}
Claude Desktop (MCP only)
Add to your claude_desktop_config.json:
macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: %APPDATA%\Claude\claude_desktop_config.json
{
"mcpServers": {
"encode": {
"command": "uvx",
"args": ["encode-toolkit"]
}
}
}
No installation needed when using
uvx. Just add the config and restart Claude.
VS Code / Copilot
Add to .vscode/mcp.json in your workspace:
{
"mcp": {
"servers": {
Tools (1)
encode_searchSearch the ENCODE database for genomic experiments and data.Configuration
{"mcpServers": {"encode": {"command": "uvx", "args": ["encode-toolkit"]}}}