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Bioinformatics DOI:10.1093/bioinformatics/btp352

The 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
Corporate Authors1000 Genome Project Data Processing Subgroup
JournalBioinformatics
Volume25
Issue16
Pages2078-9
Date Published2009 Aug 15
ISSN1367-4811
KeywordsAlgorithms, Base Sequence, Computational Biology, Genome, Genomics, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, DNA, Software
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://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=19505943
DOI10.1093/bioinformatics/btp352
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/19505943?dopt=Abstract

Alternate JournalBioinformatics
PubMed ID19505943
PubMed Central IDPMC2723002
Grant ListU54HG002750 / HG / NHGRI NIH HHS / United States
R01 HG004719-01 / HG / NHGRI NIH HHS / United States
R01 HG004719 / HG / NHGRI NIH HHS / United States
R01 HG004719-04 / HG / NHGRI NIH HHS / United States
U54 HG002750 / HG / NHGRI NIH HHS / United States
077192/Z/05/Z / / Wellcome Trust / United Kingdom
R01 HG004719-02 / HG / NHGRI NIH HHS / United States
R01 HG004719-02S1 / HG / NHGRI NIH HHS / United States
R01 HG004719-03 / HG / NHGRI NIH HHS / United States