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
| Registry | Package | Version | Transport |
|---|---|---|---|
| npm | encode-toolkit | 0.3.0-beta.5 | stdio |
| PyPI | encode-toolkit | 0.3.0b5 | stdio |
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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