ENCODE Toolkit

Overview

ENCODE Toolkit is a Model Context Protocol server that brings 20 MCP tools and 48 skills for ENCODE Project genomics directly into your AI assistant. With this server, any MCP-compatible AI can search ENCODE databases, download datasets, and orchestrate genomics pipelines in real-time conversation.

The toolkit runs entirely on your local machine via the npm package encode-toolkit, which communicates with MCP over stdio. It requires no authentication and works immediately after installation. The latest release is v0.3.0-beta.5 under AGPL-3.0 license, with source code and documentation available at ammawla/encode-toolkit on GitHub, where the project has 24 stars.

ENCODE Toolkit is categorized under Development and integrates with all major MCP clients including Claude Desktop, Claude Code, Cursor, VS Code, Windsurf, and Zed. If you maintain this project for ammawla, claim this listing to verify ownership and keep information up to date.

Installation

// claude_desktop_config.json
{
  "mcpServers": {
    "encode_toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit"
      ]
    }
  }
}