Data · Local MCP server

ENCODE Toolkit

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

What the MCP Registry states

The entry as published to the official MCP Registry (read 2026-10-04), latest version.

Registry name
io.github.ammawla/encode-toolkit
Version
0.3.0-beta.5
Status
Active
Category
data
Transport
stdio (local process)
Package
npm, PyPI
Published
2026-03-09
Updated
2026-03-09
Publisher
ammawla (GitHub)
Repository
github.com/ammawla/encode-toolkit
Source
Registry API entry

Packages

RegistryPackageVersionTransportEnvironment variables
npmencode-toolkit0.3.0-beta.5stdioNone declared
PyPIencode-toolkit0.3.0b5stdioNone declared

How to connect ENCODE Toolkit

ENCODE Toolkit runs locally from a Node.js package published to the npm registry: encode-toolkit version 0.3.0-beta.5. It speaks MCP over stdio, so the client starts it as a program and talks to it through standard input and output. It needs Node.js; clients usually start it with npx — the usual command is npx -y encode-toolkit@0.3.0-beta.5.

ENCODE Toolkit runs locally from a Python package published to PyPI: encode-toolkit version 0.3.0b5. It speaks MCP over stdio, so the client starts it as a program and talks to it through standard input and output. It needs Python; clients usually start it with uvx (from uv) or after pip install — the usual command is uvx encode-toolkit.

In the mcpServers JSON format that many desktop and editor MCP clients read, the entry looks like this (placeholders in angle brackets):

{
  "mcpServers": {
    "encode-toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit@0.3.0-beta.5"
      ]
    }
  }
}

Derived from the registry entry, not tested here. What the server does, and on what terms, is set by its publisher; check its repository or website before giving it access to your accounts or files. How to add an MCP server to an assistant · Before you connect

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