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BEDbase is a unifying platform for aggregating, analyzing and serving genomic region data as BED files. Input files are processed by a series of Python pipelines. The output of these pipelines is displayed through a RESTful API where users can access BED files along with useful statistics and plots. A project to aggregate, analyze, and serve genomic regions better (aka BED files).


Deployed public instance:



API dev:


UI dev:

Source Code:

Object store, production - base URL for cloudflare/backblaze


There's a tutorial for bedbase in the docs_jupyter folder (probably outdated).


  • bedboss: Main BEDbase processing pipeline and managing tool, combining bedqc, bedmaker, bedstat, and bedbuncher
  • bbconf: BEDbase configuration package (core of the BEDbase stack)
  • bedhost: FastAPI application with API for accessing data
  • bedhost-ui: Front-end user interface built with React
  • repository: Repository for deploying the bedhost container to AWS.
  • all_geo_beds: A subfolder, is the scripts to download all bed files on GEO using geofetch and build a backend to host the metadata using bedstat
  • geniml: Machine learning for genomic intervals