Cited by 27,437Genomics and Phylogenetic StudiesGenetics, Bioinformatics, and Biomedical ResearchGenomics and Chromatin Dynamics

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BEDTools: a flexible suite of utilities for comparing genomic features

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Quinlan, Aaron R., Hall, Ira M.·2010·Bioinformatics

DOI 10.1093/bioinformatics/btq033PMC PMC2832824

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Abstract

MOTIVATION: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. RESULTS: This article introduces a new 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. AVAILABILITY AND IMPLEMENTATION: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools CONTACT: aaronquinlan@gmail.com; imh4y@virginia.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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The Sequence Alignment/Map format and SAMtools
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Authors: Quinlan, A. R., & Hall, I. M.
Affiliations: University of Virginia (US)
Corresponding author: Quinlan, Aaron R.
Hall, Ira M.
ORCID: Quinlan, Aaron R.
Hall, Ira M.
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2010-01-28
Volume: 26
Issue: 6
Pages: 841-842
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btq033
PMC: PMC2832824
OpenAlex: W2102619694
Cited by: 27,437
References: 4
Citations by year: 2026: 2474 · 2025: 3385 · 2024: 3380 · 2023: 2862 · 2022: 2676 · 2021: 2957 · 2020: 2267 · 2019: 1731 · 2018: 1533 · 2017: 1185 · 2016: 932 · 2015: 743 · 2014: 616 · 2013: 387 · 2012: 212
FWCI: 88.15
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 2439 d)
Locations: Bioinformatics (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
Funders: Wellcome Trust
National Institutes of Health (1dp2od006493-01)
National Human Genome Research Institute (F32HG005197)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords: bedtools, BAM alignment file, genome annotation, feature overlap, next-generation sequencing data
MeSH terms: Software, Genome, Internet, Genomics

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