ENCODE Toolkit MCP Server

Search ENCODE, cross-reference 14 databases, run 7 analysis pipelines, and generate publication-ready methods - all from natural language in Claude Code. Its 20 documented tools cover encode, files, experiments, experiment. It runs locally over stdio via the published package.

People who work with encode, files and experiments and want it reachable from Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

VERIFIED ACTIVE

LAST COMMIT 2026-09-27 · ★ 21 · #121 OF 998 MAINTAINED OTHER · VERIFIED 2026-09-30

AGPL-3.0 · Python servers · how we verify → /methodology

01 · Install ENCODE Toolkit

Claude Code

claude mcp add ammawla-encode-toolkit -- npx -y encode-toolkit

Claude Desktop / Cursor / VS Code - add to config

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

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license AGPL-3.0 - declared in the repository

npm package encode-toolkit - unscoped; check the name against the project README before installing

registry namespace io.github.ammawla is GitHub-verified and matches the repo owner

03 · What ENCODE Toolkit can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can get full details for a single experiment including all files, quality metrics, and audit info, download specific files by accession to a local directory, search + download in one step. Runs in preview mode by default, and list files for a specific experiment with format/type filters.

Capability map

Tools grouped from the project's README - what ENCODE Toolkit lets an agent do.

Encode

19 tools - e.g. Search ENCODE experiments with 20+ filters.; Get full details for a single experiment including all files, quality metrics, and audit info.; Download specific files by accession to a local directory.

encode_search_experiments · encode_get_experiment · encode_download_files · encode_batch_download · encode_track_experiment · encode_list_files…

auth & access

1 tool - e.g. Store, check, or clear ENCODE credentials for restricted data access.

encode_manage_credentials

Latest releases

v0.3.4 · 2026-09-21

Reconcile pipeline skills with their workflows; fix runtime bugs and tool-call docs · Fix five server bugs; align tool versions; compute FRiP; correct every example output · Address the review findings on #19 and #20…

v0.3.3 · 2026-09-20

make the pipeline skills run on current Nextflow and correct the review findings · make the RGT data directory an explicit input

v0.3.2 · 2026-09-20

run the npm publish job on Node 24 with npm pinned to 11.x

04 · Who maintains ENCODE Toolkit

ENCODE Toolkit is maintained by ammawla. It's the only MCP server we track from this author; the repo dates to Mar 2026.

05 · Facts

repository: github.com/ammawla/encode-toolkit
category: other - ranked #121 of 998 actively-maintained other servers as of 2026-09-30.
release cadence: 4 releases in the last 90 days (latest 2026-09-21)
registry: io.github.ammawla/encode-toolkit (active, first published 2026-03-09 · 2 versions)
packages: npm:encode-toolkit · pypi:encode-toolkit

06 · ENCODE Toolkit FAQ

Is ENCODE Toolkit still maintained?

Yes - as of 2026-09-30, its last commit was 2026-09-27 and it shipped 4 releases in the last 90 days. We re-verify nightly.

What can ENCODE Toolkit do?

How do I install ENCODE Toolkit?

Run `npx -y encode-toolkit`. You can also paste the ready-made client config above.

Does ENCODE Toolkit run locally?

Yes - it's a stdio server: it runs on your machine (via npx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to ENCODE Toolkit

Alternatives to ENCODE Toolkit

Maintained other servers if ENCODE Toolkit isn't the fit.

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