Encode Toolkit
@ammawla
About 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
Config
Add this server to your MCP-compatible client using the configuration below.
{
"mcpServers": {
"encode-toolkit": {
"command": "npx",
"args": [
"encode-toolkit"
]
}
}
}Tools
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Overview
What is Encode Toolkit?
Encode Toolkit is an MCP server that provides natural language access to ENCODE genomic data, cross-references 14 external databases, runs 7 analysis pipelines, and generates publication-ready methods with full provenance tracking. It is designed for bioinformaticians and genomics researchers who want to query and analyze public genomic datasets directly from Claude Code or any MCP-compatible client.
How to use Encode Toolkit?
The recommended installation is as a Claude Code plugin: run /plugin marketplace add ammawla/encode-toolkit then /plugin install encode-toolkit inside a new Claude Code session. Alternatively, install via uvx encode-toolkit and add to your MCP client config, or use npx encode-toolkit or pip install encode-toolkit for standalone use.
Key features of Encode Toolkit
- 20 MCP tools for ENCODE data search and download
- 47 guided skills for multi-database workflows
- Integration with 14 public genomics databases
- 7 built-in analysis pipelines (ChIP-seq, ATAC-seq, etc.)
- Full provenance and audit trail for all operations
- No telemetry, no API keys required
- 98% test coverage with 568 passing tests
Use cases of Encode Toolkit
- Search for histone ChIP-seq experiments by tissue, target, or biosample
- Cross-reference GWAS variants with islet enhancers and ClinVar pathogenicity
- Download BED files from an experiment with MD5 verification
- Run a ChIP-seq pipeline with ENCODE-standard QC thresholds
- Generate a methods section with citations and provenance chain
FAQ from Encode Toolkit
What does Encode Toolkit require to run?
The server requires Python 3.10+ and can be run with uvx, npx, or a direct pip install. No API keys or environment variables are needed because it uses public REST APIs and E-utilities.
Which databases does Encode Toolkit connect to?
It connects to 14 databases: ENCODE, GTEx, ClinVar, GWAS Catalog, JASPAR, CellxGene, gnomAD, Ensembl, UCSC Genome Browser, GEO, PubMed, bioRxiv, ClinicalTrials.gov, and Open Targets.
Does Encode Toolkit collect usage data or telemetry?
No, the server explicitly states "security: no telemetry" and follows a trust-minimizing design.
Can I use Encode Toolkit with editors other than Claude Code?
Yes, it works with Claude Desktop, VS Code / Copilot, Cursor, and Windsurf by adding the appropriate MCP JSON configuration.
Frequently asked questions
What does Encode Toolkit require to run?
The server requires Python 3.10+ and can be run with `uvx`, `npx`, or a direct `pip install`. No API keys or environment variables are needed because it uses public REST APIs and E-utilities.
Which databases does Encode Toolkit connect to?
It connects to 14 databases: ENCODE, GTEx, ClinVar, GWAS Catalog, JASPAR, CellxGene, gnomAD, Ensembl, UCSC Genome Browser, GEO, PubMed, bioRxiv, ClinicalTrials.gov, and Open Targets.
Does Encode Toolkit collect usage data or telemetry?
No, the server explicitly states "security: no telemetry" and follows a trust-minimizing design.
Can I use Encode Toolkit with editors other than Claude Code?
Yes, it works with Claude Desktop, VS Code / Copilot, Cursor, and Windsurf by adding the appropriate MCP JSON configuration.
Basic information
Category
Developer Tools
License
AGPL-3.0
Transports
stdio
Author
ammawla
Submitted by
Dr. Alex M. Mawla, PhD
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