How do I install the encode toolkit mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

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ENCODE Toolkit MCP Server

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

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What is the ENCODE Toolkit MCP Server?

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

What you get

Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Maintainer setup documentation.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

Tool	What it does
encode_search_experiments
encode_get_experiment	Get full details for a single experiment including all files, quality metrics, and audit info.
encode_download_files
encode_batch_download	Search + download in one step. Runs in preview mode by default.
encode_track_experiment	Track an experiment locally with its publications, methods, and pipeline info.
encode_list_files	List files for a specific experiment with format/type filters.
encode_search_files	Search files across all experiments with combined experiment + file filters.
encode_get_metadata
encode_get_facets	Get live counts from ENCODE showing what data exists for given filters.
encode_get_file_info
encode_manage_credentials	Store, check, or clear ENCODE credentials for restricted data access.
encode_list_tracked	List all experiments in your local tracker with metadata, publication counts, and derived file counts.
encode_get_citations	Get publications for tracked experiments. Export as BibTeX or RIS for reference managers.

How to install the ENCODE Toolkit MCP Server

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

Add to claude_desktop_config.json, then restart Claude Desktop.

Example prompts to try

“Use ENCODE Toolkit to BibTeX.”
“Use ENCODE Toolkit to encode search experiments.”
“Use ENCODE Toolkit to encode get experiment.”

Frequently asked questions

20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.