Alpha 2.0
Login Register
» Articles » PMID: 21493652

BamTools: a C++ API and Toolkit for Analyzing and Managing BAM Files

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2011 Apr 16
PMID 21493652
Citations 512
Authors
Derek W Barnett
Erik K Garrison
Aaron R Quinlan
Michael P Stromberg
Gabor T Marth
Affiliations
Soon will be listed here.
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.

Citing Articles

Identification and validation of a major QTL, QFhb-6AL, for Fusarium head blight resistance on chromosome 6AL in wheat.

Zhu Z, Zhu X, Zhang N, Wang W, Liu J, Zhang F Theor Appl Genet. 2025; 138(4):74.

PMID: 40089629 DOI: 10.1007/s00122-025-04864-5.

A chromosomal-level genome assembly of Begonia fimbristipula (Begoniaceae).

Xiao T, Wang Z, Yan H Sci Data. 2025; 12(1):429.

PMID: 40074751 PMC: 11904028. DOI: 10.1038/s41597-025-04768-5.

Genome-specific association study (GSAS) for exploration of variability in hemp (Cannabis sativa).

Trubanova N, Isobe S, Shirasawa K, Watanabe A, Kelesidis G, Melzer R Sci Rep. 2025; 15(1):8371.

PMID: 40069221 PMC: 11897341. DOI: 10.1038/s41598-025-92168-5.

PBRM1 directs PBAF to pericentromeres and protects centromere integrity.

Lane K, Harrod A, Wu L, Roumeliotis T, Feng H, Foo S Nat Commun. 2025; 16(1):1980.

PMID: 40011561 PMC: 11865495. DOI: 10.1038/s41467-025-57277-9.

Hookworm genes encoding intestinal excreted-secreted proteins are transcriptionally upregulated in response to the host's immune system.

Schwarz E, Noon J, Chicca J, Garceau C, Li H, Antoshechkin I bioRxiv. 2025; .

PMID: 39975173 PMC: 11838427. DOI: 10.1101/2025.02.01.636063.

References
1.
Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View
2.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View
3.
Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A . The human genome browser at UCSC. Genome Res. 2002; 12(6):996-1006. PMC: 186604. DOI: 10.1101/gr.229102. View
4.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View
5.
Quinlan A, Hall I . BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. PMC: 2832824. DOI: 10.1093/bioinformatics/btq033. View