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The Sequence Alignment/Map format and SAMtools.

Sun, 2011-07-31 22:09 -- John Hawks
TitleThe Sequence Alignment/Map format and SAMtools.
Publication TypeJournal Article
Year of Publication2009
AuthorsLi, H, Handsaker, B, Wysoker, A, Fennell, T, Ruan, J, Homer, N, Marth, G, Abecasis, G, Durbin, R, Subgroup}, GPDP{1000
JournalBioinformatics (Oxford, England)
Volume25
Pagination2078–2079
Date Publishedaug
ISSN1367-4811
Keywords2010-10-16, bioinformatics, genomics, software, tools
Abstract

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.
URLhttp://dx.doi.org/10.1093/bioinformatics/btp352
DOI10.1093/bioinformatics/btp352
Citation KeyLi:SAMtools:2009

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