20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines
ENCODE Toolkit MCP server exists for a simple reason — assistants are far more useful when they can act on ENCODE Toolkit directly instead of describing what you should do. 20 MCP tools + 48 skills for ENCODE Project genomics — search, download, pipelines.
Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods — all from natural language in Claude Code.
Installation goes through your MCP client rather than a global install: point it at encode-toolkit on npm and it is fetched when the client starts. The copy-paste blocks for Claude Desktop, Claude Code and Cursor are further down this page.
Once ENCODE Toolkit is connected, these are the calls the assistant has available:
BibTeX — The BibTeX tool exposed by this serverencode_search_experiments — The encode_search_experiments tool exposed by this serverencode_get_experiment — Get full details for a single experiment including all files, quality metrics, and audit infoencode_download_files — The encode_download_files tool exposed by this serverencode_batch_download — Search + download in one step. Runs in preview mode by defaultencode_track_experiment — Track an experiment locally with its publications, methods, and pipeline infoencode_list_files — List files for a specific experiment with format/type filtersencode_search_files — Search files across all experiments with combined experiment + file filtersencode_get_metadata — The encode_get_metadata tool exposed by this serverencode_get_facets — Get live counts from ENCODE showing what data exists for given filtersencode_get_file_info — The encode_get_file_info tool exposed by this serverencode_manage_credentials — Store, check, or clear ENCODE credentials for restricted data accessAmong the developer tooling options, the useful question is rarely "what can it do" but "what does it cost you to run" — permissions, credentials, and how much of your context its toolset consumes. ENCODE Toolkit's toolset — BibTeX, encode_search_experiments, encode_get_experiment and 11 more — is a fair guide to whether it matches your workflow. It is maintained by ammawla; worth a glance at recent repository activity before you build anything load-bearing on it.
SyncDev reviews every entry in this directory against the project's own documentation before publishing, and revisits them as servers change.
| Tool | What it does |
|---|---|
| BibTeX | The BibTeX tool exposed by this server. |
| encode_search_experiments | The encode_search_experiments tool exposed by this server. |
| encode_get_experiment | Get full details for a single experiment including all files, quality metrics, and audit info. |
| encode_download_files | The encode_download_files tool exposed by this server. |
| 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 | The encode_get_metadata tool exposed by this server. |
| encode_get_facets | Get live counts from ENCODE showing what data exists for given filters. |
| encode_get_file_info | The encode_get_file_info tool exposed by this server. |
| 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. |
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": ["-y", "encode-toolkit"]
}
}
}Add to claude_desktop_config.json, then restart Claude Desktop.
Kill hallucinated APIs — version-accurate, up-to-date library documentation injected straight into context.
Microsoft's official browser automation server — drive a real browser through the accessibility tree, no screenshots needed.
GitHub's official server — repos, issues, pull requests, Actions and code security, straight from your assistant.
Issue tracking at the speed of conversation — Linear's official hosted server with OAuth and zero install.
Local repository surgery — status, diffs, commits, branches and history for any repo on disk.
Timezone sanity for AI — current time anywhere and correct conversions, without the model doing date math.