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Bioinformatics (Oxford, England) 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, 1000 Genome Project Data Processing, S
JournalBioinformatics (Oxford, England)
Volume25
Issue16
Pages2078-9
Date Published2009/08/15
ISSN1367-4803
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