BEDTools: a flexible suite of utilities for comparing genomic features

The paper presents BEDTools, a flexible software suite for comparing, manipulating, and annotating genomic features stored in Browser Extensible Data (BED) and General Feature Format (GFF), addressing the fundamental genomics task of testing for overlaps and correlations between different sets of features. Beyond BED and GFF, the suite supports comparing sequence alignments in BAM format against these feature formats, and it is implemented in C++ for efficiency.

BEDTools is extremely efficient and lets users compare very large datasets, such as next-generation sequencing output, against both public and custom genome annotation tracks that were awkward to handle with existing web-based methods. Because its utilities can be combined with one another and with standard UNIX commands, BEDTools streamlines routine genomics work and supports pipelines that quickly answer intricate questions of large genomic datasets, with source code and a comprehensive manual freely available.