BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit

BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.

You can read more about BEDOPS and how it can be useful for your research in the Overview documentation, as well as in the original manuscript.

  • bedops - apply set operations on any number of BED inputs
  • bedextract - efficiently extract BED features
  • closest-features - matches nearest features between BED files
  • bedmap - map overlapping BED elements onto target regions and optionally compute any number of common statistical operations


If you use BEDOPS in your research, please cite the following manuscript:

Shane Neph, M. Scott Kuehn, Alex P. Reynolds, et al. BEDOPS: high-performance genomic feature operations. Bioinformatics (2012) 28 (14): 1919-1920. doi: 10.1093/bioinformatics/bts277