ENCODE Toolkit
ENCODE Toolkit is a MCP server for web research and discovery, published by ammawla.
MCP server and Claude plugin providing 20 tools and 47 skills for ENCODE genomics data access, analysis pipelines, database cross-reference, and publication-ready provenance tracking.
Is it any good?
Effectiveness · benchmark pending
We haven't benchmarked ENCODE Toolkit yet, so its score is provisional — computed from safety, maintenance, and documentation only, with popularity given no weight. When we benchmark it, we measure whether it produces materially better output than a frontier model alone, and that result leads the score. How we measure.
About ENCODE Toolkit
Description · AI-summarised from the ammawla README
ENCODE Toolkit is a comprehensive genomics research automation platform for Claude that integrates the ENCODE database with 13 other major bioinformatics databases (GTEx, ClinVar, GWAS Catalog, JASPAR, CellxGene, gnomAD, Ensembl, UCSC Genome Browser, GEO, PubMed, bioRxiv, ClinicalTrials.gov, Open Targets). It provides 20 MCP tools for searching, downloading, and tracking genomic experiments; 47 workflow skills for common analyses like quality assessment, integrative analysis, regulatory element discovery, and epigenome profiling; and 7 analysis pipelines (ChIP-seq, ATAC-seq, RNA-seq, Hi-C, WGBS, CUT&RUN, CUT&TAG). Features include batch downloads with MD5 verification, experiment tracking with citations, provenance chains from derived files back to source data, and methods section generation with full audit trail. Evidence-based quality thresholds are backed by primary literature (Landt 2012, Buenrostro 2013, Ernst & Kellis 2012, ENCODE Phase 3 2020). Available as Claude plugin, MCP server, and Python/Node package.
Where it fits
Browse related skills
Install ENCODE Toolkit
Install
Install via MCP server
{
"mcpServers": {
"ammawla-encode-toolkit": {
"command": "npx",
"args": ["-y", "@ammawla/ammawla-encode-toolkit"]
}
}
}Install with your AI
Zero install · paste into ChatGPT, Claude, Cursor…
Install the "ENCODE Toolkit" skill into my project by following all instructions at https://skillsdirectory.co/s/ammawla-encode-toolkit
Your assistant reads /s/ammawla-encode-toolkit and follows it — fetching the files from the source, placing them, and confirming before it runs anything. No account needed. How this works.
Frequently asked
FAQ
What does ENCODE Toolkit do?
MCP server and Claude plugin providing 20 tools and 47 skills for ENCODE genomics data access, analysis pipelines, database cross-reference, and publication-ready provenance tracking.
How do I install ENCODE Toolkit?
ENCODE Toolkit is a MCP server. Primary install path: { "mcpServers": { "ammawla-encode-toolkit": { "command": "npx", "args": ["-y", "@ammawla/ammawla-encode-toolkit"] } } }
What is the Skill Score for ENCODE Toolkit?
ENCODE Toolkit has a Skill Score of 5.9/10 (Solid). It is currently a provisional score — ENCODE Toolkit hasn't been benchmarked yet, so it weights safety 75/100 (40%), maintenance 56/100 (30%), and documentation 70/100 (30%). Popularity carries zero weight until effectiveness is measured. See methodology.
Is ENCODE Toolkit free?
ENCODE Toolkit is published under the AGPL-3.0 license. See the vendor's source repository for any usage limits or paid tiers.
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Embed this score
For maintainers · always-current, links back
Put it in your README — it updates as the score changes.[](https://skillsdirectory.co/skills/ammawla-encode-toolkit)
<a href="https://skillsdirectory.co/skills/ammawla-encode-toolkit"><img src="https://skillsdirectory.co/badge/ammawla-encode-toolkit.svg" alt="Scored by skillsdirectory" height="28" /></a>