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BEDTools | A flexible suite of utilities for comparing genomic features

A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets.

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Fabien Pichon

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Another indispensable tools suite to have, particularly if you work with .bed files, of course !
In comparison, however, Homer is better if you want to intersect further files because it gives more details, ideal to create a Venn diagram !
A big plus of bedtools : tools are very well documented, with schemes ! I like: "shuffle" to randomly relocate peaks, to test significance of a pathway enrichment for example !

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BEDTools classification

BEDTools specifications

Unique identifier:
Command line interface
Operating system:
GNU General Public License version 2.0
Software type:
Restrictions to use:
Programming languages:
Computer skills:


  • coverageBed

BEDTools distribution


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BEDTools support



  • Aaron R. Quinlan <>


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Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine and Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA

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