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.

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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}
}

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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": {
      "encode": {
        "command": "uvx",
        "args": ["encode-toolkit"]
      }
    }
  }
}

Cursor

Add to .cursor/mcp.json:

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

Windsurf

Add to .windsurf/mcp.json:

{
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

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Connected Databases

ENCODE Toolkit integrates 14 databases through live API tools and guided skills.