ENCODE Toolkit

local MCP server

Installation

Terminal

claude mcp add encode-toolkit -- npx -y encode-toolkit

Run in your project folder. Add --scope user to use it everywhere.

Add to claude_desktop_config.json or .cursor/mcp.json.

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

20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines

ENCODE Toolkit is a local MCP server distributed as the npm package encode-toolkit.

Run: claude mcp add encode-toolkit -- npx -y encode-toolkit

Run: codex mcp add encode-toolkit -- npx -y encode-toolkit

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