Sambamba: fast processing of NGS alignment formats

Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces proc...

Full description

Saved in:
Bibliographic Details
Published inBioinformatics (Oxford, England) Vol. 31; no. 12; pp. 2032 - 2034
Main Authors Tarasov, Artem, Vilella, Albert J., Cuppen, Edwin, Nijman, Isaac J., Prins, Pjotr
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.06.2015
Subjects
Algorithms
Applications Notes
EPS-2
Genomics
High-Throughput Nucleotide Sequencing - methods
Humans
Laboratorium voor Nematologie
Laboratory of Nematology
Sequence Alignment
Sequence Analysis, DNA - methods
Software
Online AccessGet full text

Cover

More Information
Summary:Sambamba is a high-performance robust tool and library for working with SAM, BAM and CRAM sequence alignment files; the most common file formats for aligned next generation sequencing data. Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time. Sambamba is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability. Availability and implementation: Sambamba is free and open source software, available under a GPLv2 license. Sambamba can be downloaded and installed from http://www.open-bio.org/wiki/Sambamba. Sambamba v0.5.0 was released with doi:10.5281/zenodo.13200. Contact: j.c.p.prins@umcutrecht.nl
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Associate Editor: Inanc Birol
ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btv098