ENCODE Toolkit

A Claude Code plugin (and standalone MCP server) that searches, downloads, and analyzes ENCODE Project functional-genomics data, bundling 20 MCP tools with seven reference analysis pipelines.

   
Type Claude Code Plugin (bundles an MCP server + workflow skills)
Supplier ammawla
Availability Beta — PyPI v0.3.0 (2026-03-21)
Pricing Free / OSS (AGPL-3.0-only)
Capabilities Read/Write — read-only ENCODE API queries; writes downloaded files and local experiment-tracking records to disk
Verified works · 2026-07-20
Security caution · 2026-07-20 — provenance matches ammawla, maintained, but AGPL-3.0-only copyleft and unaffiliated community project

How to install

The plugin path installs the MCP server and the 47 workflow skills + 7 pipelines. The MCP-only path installs just the 20 tools.

  • Prerequisite — uv (provides uvx) or Python with pip, plus Claude Code. uvx fetches and runs encode-toolkit on demand, so no separate install step is required for the MCP-only path.

  • Claude Code — plugin marketplace (recommended; includes skills + pipelines): 
    /plugin marketplace add ammawla/encode-toolkit
/plugin install encode-toolkit

    (Plugin-shipped skills resolve as /encode-toolkit:<skill>, not bare /<skill>.)

  • Claude Code — MCP server only (20 tools, no skills): 
    claude mcp add encode -- uvx encode-toolkit

    Claude Code launches uvx encode-toolkit itself over stdio — do not run it separately.

  • Claude Desktop — add to claude_desktop_config.json (Claude Desktop has no plugin-marketplace path, so this gives the MCP tools only): 
    {
  "mcpServers": {
    "encode": {
      "command": "uvx",
      "args": ["encode-toolkit"]
    }
  }
}

    (If uvx is not on Claude Desktop’s PATH, install the package first with pip install encode-toolkit and set "command": "encode-toolkit" with "args": [].)

What it does

Twenty MCP tools front the live ENCODE Portal REST API — including encode_search_experiments (20+ filters), encode_get_experiment, encode_list_files / encode_search_files, encode_get_metadata / encode_get_facets (valid filter values and live availability counts), encode_download_files (with MD5 verification), encode_batch_download (search + download in one call), and encode_track_experiment (local tracking with linked publications), plus tools for compatibility and provenance analysis.

The plugin also ships seven reference analysis pipelines, each with staged reference files and a Nextflow DSL2 workflow:

  • ChIP-seq (BWA-MEM, MACS2 + IDR)
  • ATAC-seq (Bowtie2, MACS2 with Tn5 adjustment)
  • RNA-seq (STAR, RSEM + Kallisto)
  • WGBS methylation (Bismark, MethylDackel)
  • Hi-C (BWA, Juicer + HiCCUPS)
  • DNase-seq (BWA, Hotspot2)
  • CUT&RUN (Bowtie2, SEACR)

Primary use cases: querying and bulk-downloading ENCODE functional-genomics data, scaffolding ChIP/ATAC/RNA-seq/Hi-C/WGBS/CUT&RUN analyses, annotating regions with regulatory tracks.

Notes

Community project, not ENCODE- or vendor-affiliated. Most ENCODE data is public and needs no API key; restricted-data credentials, when used, are stored in the OS keyring. The package advertises integration with 14 databases (ENCODE plus GTEx, ClinVar, GWAS Catalog, JASPAR, CellxGene, gnomAD, Ensembl, UCSC, GEO, PubMed, bioRxiv, and others), but the 20 live MCP tools target the ENCODE Portal; the other sources appear in the bundled pipeline/skill references. Licensed AGPL-3.0 — network use of a modified version triggers the AGPL source-availability obligation; review before deploying a modified copy as a service. This entry is distinct from the read-only ENCODE REST-API Claude Skill catalogued at ENCODE (Claude Skill): this toolkit adds download management, local tracking, and executable pipelines.

Sources

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