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Bioinformatics. 2015 Jun 15;31(12):2032-4. doi: 10.1093/bioinformatics/btv098. Epub 2015 Feb 19.

Sambamba: fast processing of NGS alignment formats.

Author information

1
Department of Statistical Simulation, St. Petersburg State University, St. Petersburg, Russia, Illumina Cambridge, Cambridge, UK, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands, Department of Medical Genetics, Institute for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands and Department of Nematology, Wageningen University, Wageningen, The Netherlands.
2
Department of Statistical Simulation, St. Petersburg State University, St. Petersburg, Russia, Illumina Cambridge, Cambridge, UK, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands, Department of Medical Genetics, Institute for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands and Department of Nematology, Wageningen University, Wageningen, The Netherlands Department of Statistical Simulation, St. Petersburg State University, St. Petersburg, Russia, Illumina Cambridge, Cambridge, UK, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands, Department of Medical Genetics, Institute for Molecular Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands and Department of Nematology, Wageningen University, Wageningen, The Netherlands.

Abstract

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.

PMID:
25697820
PMCID:
PMC4765878
DOI:
10.1093/bioinformatics/btv098
[Indexed for MEDLINE]
Free PMC Article

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