Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Bioinformatics. 2011 Dec 15;27(24):3423-4. doi: 10.1093/bioinformatics/btr539. Epub 2011 Sep 23.


Summary: pybedtools is a flexible Python software library for manipulating and exploring genomic datasets in many common formats. It provides an intuitive Python interface that extends upon the popular BEDTools genome arithmetic tools. The library is well documented and efficient, and allows researchers to quickly develop simple, yet powerful scripts that enable complex genomic analyses.

Availability: pybedtools is maintained under the GPL license. Stable versions of pybedtools as well as documentation are available on the Python Package Index at


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Animals
  • Computational Biology
  • Genomics
  • Molecular Sequence Annotation
  • Software*