refgenie: reference genome data management

refgenie is a catalog of reference genomes and the files built from them: FASTA files, aligner indexes and annotations. Each genome is identified by a GA4GH sequence collection digest computed from its sequences. The refgenie command-line tool downloads these files and tells your pipeline where they are. This page is a JavaScript app; without JavaScript, use these links.

• llms.txt: an index for AI agents.
• SKILL.md for the HTTP API and SKILL.md for the command line.
• MCP server: https://api.refgenie.org/mcp (Streamable HTTP, read-only). Setup guide.
• Documentation

The data on these pages, as JSON: a search is https://api.refgenie.org/v4/genomes?q=hg38, the page /genomes/{digest} is https://api.refgenie.org/v4/genomes/{digest}, and its assets are https://api.refgenie.org/v4/assets?genome_digest={digest}.

Missing a genome or an asset? Request it on refgenie-registry.