The Sequence Alignment/Map format and SAMtools

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and...

Descripción completa

Detalles Bibliográficos
Autores principales: Li, Heng, Handsaker, Bob, Wysoker, Alec, Fennell, Tim, Ruan, Jue, Homer, Nils, Marth, Gabor, Abecasis, Goncalo, Durbin, Richard
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/
https://www.ncbi.nlm.nih.gov/pubmed/19505943
http://dx.doi.org/10.1093/bioinformatics/btp352
_version_ 1782170346899636224
author Li, Heng
Handsaker, Bob
Wysoker, Alec
Fennell, Tim
Ruan, Jue
Homer, Nils
Marth, Gabor
Abecasis, Goncalo
Durbin, Richard
author_facet Li, Heng
Handsaker, Bob
Wysoker, Alec
Fennell, Tim
Ruan, Jue
Homer, Nils
Marth, Gabor
Abecasis, Goncalo
Durbin, Richard
author_sort Li, Heng
collection PubMed
description Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
format Text
id pubmed-2723002
institution National Center for Biotechnology Information
language English
publishDate 2009
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-27230022009-08-07 The Sequence Alignment/Map format and SAMtools Li, Heng Handsaker, Bob Wysoker, Alec Fennell, Tim Ruan, Jue Homer, Nils Marth, Gabor Abecasis, Goncalo Durbin, Richard Bioinformatics Applications Note Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk Oxford University Press 2009-08-15 2009-06-08 /pmc/articles/PMC2723002/ /pubmed/19505943 http://dx.doi.org/10.1093/bioinformatics/btp352 Text en http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Li, Heng
Handsaker, Bob
Wysoker, Alec
Fennell, Tim
Ruan, Jue
Homer, Nils
Marth, Gabor
Abecasis, Goncalo
Durbin, Richard
The Sequence Alignment/Map format and SAMtools
title The Sequence Alignment/Map format and SAMtools
title_full The Sequence Alignment/Map format and SAMtools
title_fullStr The Sequence Alignment/Map format and SAMtools
title_full_unstemmed The Sequence Alignment/Map format and SAMtools
title_short The Sequence Alignment/Map format and SAMtools
title_sort sequence alignment/map format and samtools
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002/
https://www.ncbi.nlm.nih.gov/pubmed/19505943
http://dx.doi.org/10.1093/bioinformatics/btp352
work_keys_str_mv AT liheng thesequencealignmentmapformatandsamtools
AT handsakerbob thesequencealignmentmapformatandsamtools
AT wysokeralec thesequencealignmentmapformatandsamtools
AT fennelltim thesequencealignmentmapformatandsamtools
AT ruanjue thesequencealignmentmapformatandsamtools
AT homernils thesequencealignmentmapformatandsamtools
AT marthgabor thesequencealignmentmapformatandsamtools
AT abecasisgoncalo thesequencealignmentmapformatandsamtools
AT durbinrichard thesequencealignmentmapformatandsamtools
AT thesequencealignmentmapformatandsamtools
AT liheng sequencealignmentmapformatandsamtools
AT handsakerbob sequencealignmentmapformatandsamtools
AT wysokeralec sequencealignmentmapformatandsamtools
AT fennelltim sequencealignmentmapformatandsamtools
AT ruanjue sequencealignmentmapformatandsamtools
AT homernils sequencealignmentmapformatandsamtools
AT marthgabor sequencealignmentmapformatandsamtools
AT abecasisgoncalo sequencealignmentmapformatandsamtools
AT durbinrichard sequencealignmentmapformatandsamtools
AT sequencealignmentmapformatandsamtools

Ejemplares similares