ammawla/encode-toolkit

Overview

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

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

How to use

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

Tested with

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

Notes

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.

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

Use cases

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

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

Indexed from awesome-mcp-servers-punkpeye and enriched against its public facts.