Sambamba: fast processing of NGS alignment formats

Artem Tarasov; Albert J Vilella; Edwin Cuppen; Isaac J Nijman; Pjotr Prins

doi:10.1093/bioinformatics/btv098

Sambamba: fast processing of NGS alignment formats

Artem Tarasov, Albert J Vilella, Edwin Cuppen, Isaac J Nijman, Pjotr Prins

Hubrecht Institute

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

1182 Citaten (Scopus)

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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: [email protected].

Originele taal-2	Engels
Tijdschrift	Bioinformatics
DOI's	https://doi.org/10.1093/bioinformatics/btv098
Status	Gepubliceerd - 19 feb. 2015

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title = "Sambamba: fast processing of NGS alignment formats",

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.CONTACT: [email protected].",

author = "Artem Tarasov and Vilella, {Albert J} and Edwin Cuppen and Nijman, {Isaac J} and Pjotr Prins",

note = "{\textcopyright} The Author 2015. Published by Oxford University Press.",

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doi = "10.1093/bioinformatics/btv098",

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AU - Vilella, Albert J

AU - Cuppen, Edwin

AU - Nijman, Isaac J

AU - Prins, Pjotr

PY - 2015/2/19

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AB - 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: [email protected].

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Sambamba: fast processing of NGS alignment formats

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