Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Jun 15;27(12):1691-2.
doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14.

BamTools: a C++ API and toolkit for analyzing and managing BAM files

Derek W Barnett  1 , Erik K Garrison, Aaron R Quinlan, Michael P Strömberg, Gabor T Marth
Affiliations

BamTools: a C++ API and toolkit for analyzing and managing BAM files

Derek W Barnett et al. Bioinformatics. .

Abstract

Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.

Results: We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit.

Availability: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

PubMed Disclaimer

References

    1. The 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010;467:1061–1073. - PMC - PubMed
    1. Kent WJ, et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1106. - PMC - PubMed
    1. Li H, et al. The sequence alignment/map format and SAMtools. Bionformatics. 2009;25:2078–2079. - PMC - PubMed
    1. McKenna A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303. - PMC - PubMed
    1. Quinlan AR, et al. BEDTools: a flexible suite of utilities for comparing genomic features. Bionformatics. 2010;26:841–842. - PMC - PubMed

Publication types