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bedtools - a swiss army knife for genome arithmetic

Current version: 2.18.2

Note

Stable release for bedtools were formerly archived on Google Code. Unfortunately, the Google Code downloads facility is shutting down; so henceforth, all source code and stable releases will be maintained via this Github repository.

Summary

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.

While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Details

First created through urgency and adrenaline by Aaron Quinlan Spring 2009. Maintained by the Quinlan Laboratory at the University of Virginia.

  1. Lead developers: Aaron Quinlan, Neil Kindlon
  2. Significant contributions: Assaf Gordon, Royden Clark, John Marshall, Brent Pedersen, Ryan Dale
  3. Repository: https://github.com/arq5x/bedtools2
  4. Stable releases: https://github.com/arq5x/bedtools2/releases
  5. Documentation: http://bedtools.readthedocs.org
  6. License: Released under GNU public license version 2 (GPL v2).

Citation

Please cite the following article if you use BEDTools in your research:
  • Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
Also, if you use pybedtools, please cite the following.
  • Dale RK, Pedersen BS, and Quinlan AR. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics (2011). doi:10.1093/bioinformatics/btr539