BEDTools

BEDTools is a software suite that allows for the comparison, manipulation, and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF). It also supports the comparison of sequence alignments in BAM format to both BED and GFF features. BEDTools is efficient and allows users to compare large datasets and custom genome annotation tracks, and can be combined with UNIX commands for complex questions of large genomic datasets.

Topic

Genomics

Detail

  • Operation: Mapping

  • Software interface: Suite

  • Language: ;BEDTools is an extensive suite of utilities for comparing genomic features in BED format.;Suite;C++

  • License: MIT license

  • Cost: Free

  • Version name: 2.30.0

  • Credit: Ruth L. Kirschstein National Research Service Award from the National Institutes of Health, Burroughs Wellcome Fund Career Award, National Institutes of Health Directors New Innovator Award.

  • Input: -

  • Output: -

  • Contact: aaronquinlan@gmail.com; imh4y@virginia.edu

  • Collection: -

  • Maturity: Mature

Publications

  • BEDTools: a flexible suite of utilities for comparing genomic features.
  • Quinlan AR and Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. BEDTools: a flexible suite of utilities for comparing genomic features. 2010; 26:841-2. doi: 10.1093/bioinformatics/btq033
  • https://doi.org/10.1093/bioinformatics/btq033
  • PMID: 20110278
  • PMC: PMC2832824

Download and documentation

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