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...
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| Published in | Bioinformatics (Oxford, England) Vol. 31; no. 12; pp. 2032 - 2034 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
15.06.2015
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| Subjects | |
| Online Access | Get full text |
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| 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: j.c.p.prins@umcutrecht.nl |
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| AbstractList | 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 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.UNLABELLEDSambamba 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.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.AVAILABILITY AND IMPLEMENTATIONSambamba 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. 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. 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. 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 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. |
| Author | Vilella, Albert J. Cuppen, Edwin Tarasov, Artem Prins, Pjotr Nijman, Isaac J. |
| Author_xml | – sequence: 1 givenname: Artem surname: Tarasov fullname: Tarasov, Artem – sequence: 2 givenname: Albert J. surname: Vilella fullname: Vilella, Albert J. – sequence: 3 givenname: Edwin surname: Cuppen fullname: Cuppen, Edwin – sequence: 4 givenname: Isaac J. surname: Nijman fullname: Nijman, Isaac J. – sequence: 5 givenname: Pjotr surname: Prins fullname: Prins, Pjotr |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25697820$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1093/bioinformatics/btu390 10.1038/nbt0308-256b 10.1093/bioinformatics/btu314 10.1038/nrg2857-c1 10.1093/nar/gks1175 10.1186/1751-0473-9-13 10.4103/2153-3539.103013 10.1093/bioinformatics/btp352 |
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| References | Cochrane (2023020115240872800_btv098-B3) 2013; 41 Trelles (2023020115240872800_btv098-B12) 2011; 12 Prins (2023020115240872800_btv098-B8) 2014 Gullapalli (2023020115240872800_btv098-B5) 2012; 3 Picard (2023020115240872800_btv098-B7) 2009 Tischler (2023020115240872800_btv098-B11) 2014; 9 Bonfield (2023020115240872800_btv098-B2) 2014; 30 Alexandrescu (2023020115240872800_btv098-B1) 2010 Li (2023020115240872800_btv098-B6) 2009; 25 Siva (2023020115240872800_btv098-B9) 2008; 26 Faust (2023020115240872800_btv098-B4) 2014; 30 Thurston (2023020115240872800_btv098-B10) 2006 24812344 - Bioinformatics. 2014 Sep 1;30(17):2503-5 19505943 - Bioinformatics. 2009 Aug 15;25(16):2078-9 18327223 - Nat Biotechnol. 2008 Mar;26(3):256 21301471 - Nat Rev Genet. 2011 Mar;12(3):224 24930138 - Bioinformatics. 2014 Oct;30(19):2818-9 23248761 - J Pathol Inform. 2012;3:40 23203883 - Nucleic Acids Res. 2013 Jan;41(Database issue):D30-5 |
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| Title | Sambamba: fast processing of NGS alignment formats |
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