Sambamba: fast processing of NGS alignment formats

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 red...

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Autores principales: Tarasov, Artem, Vilella, Albert J., Cuppen, Edwin, Nijman, Isaac J., Prins, Pjotr
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765878/
https://www.ncbi.nlm.nih.gov/pubmed/25697820
http://dx.doi.org/10.1093/bioinformatics/btv098
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author Tarasov, Artem
Vilella, Albert J.
Cuppen, Edwin
Nijman, Isaac J.
Prins, Pjotr
author_facet Tarasov, Artem
Vilella, Albert J.
Cuppen, Edwin
Nijman, Isaac J.
Prins, Pjotr
author_sort Tarasov, Artem
collection PubMed
description 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
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spelling pubmed-47658782016-03-04 Sambamba: fast processing of NGS alignment formats Tarasov, Artem Vilella, Albert J. Cuppen, Edwin Nijman, Isaac J. Prins, Pjotr Bioinformatics Applications Notes 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 Oxford University Press 2015-06-15 2015-02-19 /pmc/articles/PMC4765878/ /pubmed/25697820 http://dx.doi.org/10.1093/bioinformatics/btv098 Text en © The Author 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Tarasov, Artem
Vilella, Albert J.
Cuppen, Edwin
Nijman, Isaac J.
Prins, Pjotr
Sambamba: fast processing of NGS alignment formats
title Sambamba: fast processing of NGS alignment formats
title_full Sambamba: fast processing of NGS alignment formats
title_fullStr Sambamba: fast processing of NGS alignment formats
title_full_unstemmed Sambamba: fast processing of NGS alignment formats
title_short Sambamba: fast processing of NGS alignment formats
title_sort sambamba: fast processing of ngs alignment formats
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765878/
https://www.ncbi.nlm.nih.gov/pubmed/25697820
http://dx.doi.org/10.1093/bioinformatics/btv098
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