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ammawla/encode-toolkit

MCP server and Claude Plugin for a full ENCODE Project genomic data and analysis toolkit — search, download, track, and analyze functional genomics experiments

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Our verdict

Not reviewed yet

We have not reviewed ammawla/encode-toolkit yet

No one at Enterprise DNA has checked this listing against its sources. The description comes from public listings gathered automatically. Any fact below shows where it came from and when it was last checked.

How we review records

From the listing

About ammawla/encode-toolkit

This tool provides an MCP server and Claude plugin for accessing the ENCODE Project genomic data. It allows users to search, download, track, and analyze functional genomics experiments programmatically. The toolkit is written in Python and integrates with Claude for natural language interactions.

Best for

Developers and bioinformaticians who need to query and retrieve ENCODE genomic data through Claude or programmatic interfaces

Use cases

  • Search ENCODE functional genomics experiments by metadata
  • Download genomic datasets directly into analysis pipelines
  • Track experiment status and metadata through Claude chat

Notes

35 stars on GitHub. Last updated 2026-05-08. Licensed AGPL-3.0.

Pros

  • Integrates with Claude for natural language queries
  • Provides programmatic access to a large public genomic database
  • Open source Python toolkit with straightforward setup

Cons

  • Low star count indicates limited community adoption
  • Documentation and examples may be sparse
  • Only supports ENCODE data, not other genomic repositories

Key facts

What we have checked

Days since the last commit
29
Checked GitHub
GitHub forks
5
Checked GitHub
GitHub stars
22
Checked GitHub
Open issues
0
Checked GitHub
Releases in the last 90 days
4
Checked GitHub

Each value shows when we last confirmed it and where it came from. Values we have not confirmed are left out, never guessed.

How to use

How to set it up

As the listing publishes it. We have not run this install.

Install

npx encode-toolkit

Tools exposed

  • assay_title
  • biosample_type
  • biosample_term_name
  • file_accessions
  • download_dir
  • organize_by
  • verify_md5
  • file_format
  • dry_run
  • fetch_publications
  • fetch_pipelines
  • experiment_accession
  • output_type
  • preferred_default
  • metadata_type
  • access_key
  • secret_key
  • export_format
  • file_path
  • source_accessions

Clients the listing names (not checked here)

Claude Desktop, Claude Code, Cursor, Windsurf, VS Code

Install

Add ammawla/encode-toolkit to your client

Not verified yet

Our lab has not run this server yet. "Config checked" on a client means the recipe matches that client's documented config format; it does not mean we ran it.

Claude Code

Config checked

Run in your terminal (runs on your computer)

claude mcp add --transport stdio ammawla-encode-toolkit -- npx -y encode-toolkit@0.3.0-beta.5

Version 0.3.0-beta.5 · From the Official MCP registry, read · Format checked against Claude Code's config docs

Claude Desktop

Config checked

Add to claude_desktop_config.json (runs on your computer)

{
  "mcpServers": {
    "ammawla-encode-toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit@0.3.0-beta.5"
      ]
    }
  }
}

Version 0.3.0-beta.5 · From the Official MCP registry, read · Format checked against Claude Desktop's config docs

Cursor

Config checked

Add to .cursor/mcp.json (runs on your computer)

{
  "mcpServers": {
    "ammawla-encode-toolkit": {
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit@0.3.0-beta.5"
      ]
    }
  }
}

Version 0.3.0-beta.5 · From the Official MCP registry, read · Format checked against Cursor's config docs

VS Code

Config checked

Add to .vscode/mcp.json (runs on your computer)

{
  "servers": {
    "ammawla-encode-toolkit": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "encode-toolkit@0.3.0-beta.5"
      ]
    }
  }
}

Version 0.3.0-beta.5 · From the Official MCP registry, read · Format checked against VS Code's config docs

Codex

Config checked

Add to ~/.codex/config.toml (runs on your computer)

[mcp_servers.ammawla-encode-toolkit]
command = "npx"
args = ["-y", "encode-toolkit@0.3.0-beta.5"]

Version 0.3.0-beta.5 · From the Official MCP registry, read · Format checked against Codex's config docs

  • ChatGPT: ChatGPT connects only to remote servers that need no API key.

Recipes come from the server's entry in the official MCP registry. Check the package name before you run it, and keep keys out of shared files.

Works with

What ammawla/encode-toolkit connects to

5 clients, each with how we know and when we checked.

Works withTypeHow we knowChecked
Claude CodeClientInstall recipe matches the client's documented formatRuns locally, version 0.3.0-beta.5Config checkedClaude Code docs
Claude DesktopClientInstall recipe matches the client's documented formatRuns locally, version 0.3.0-beta.5Config checkedClaude Desktop docs
CursorClientInstall recipe matches the client's documented formatRuns locally, version 0.3.0-beta.5Config checkedCursor docs
VS CodeClientInstall recipe matches the client's documented formatRuns locally, version 0.3.0-beta.5Config checkedVS Code docs
CodexClientInstall recipe matches the client's documented formatRuns locally, version 0.3.0-beta.5Config checkedCodex docs

Health and security

Is ammawla/encode-toolkit looked after, and what do its setup files show

Health score

56 out of 100

Does someone look after this repository? It does not say the code is good or safe. Worked out from GitHub signals checked . How it is worked out

PartPointsWhat we saw
Recent activity30 of 30Last push 29 days ago
Releases15 of 154 releases in 90 days
Issue repliesNot countedThe latest check has no issue response reading (fewer than 3 measured issues, or issues switched off)
Maintainer0 of 15Owned by a single user
Official source0 of 20Community server

Sources

Where this comes from

  • GitHubRegistry

    Checked · Days since the last commit, GitHub forks, GitHub stars, Open issues, Releases in the last 90 days

A source shows what was published when we checked it. It does not certify security, performance or a working installation. Read our method.

Changelog

What changed

No changes recorded yet. Releases, price changes and deprecations appear here, with their dates, once we track them for this record.

Pairs with

Other entries in the index that connect to this one. Click through to see the chain.

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