The Sequence Alignment/Map format and SAMtools.

Bioinformatics
Authors
Heng Li
Bob Handsaker
Alec Wysoker
Tim Fennell
Jue Ruan
Nils Homer
Gabor Marth
Goncalo Abecasis
Richard Durbin
1000 Genome Project Data Processing Subgroup
Keywords
Base Sequence
Computational Biology
Genome
Genomics
Algorithms
Molecular Sequence Data
Sequence Alignment
Software
Sequence Analysis, DNA
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.
Year of Publication
2009
Journal
Bioinformatics
Volume
25
Issue
16
Pages
2078-9
Date Published
2009 Aug 15
ISSN
1367-4811
URL
http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=19505943
DOI
10.1093/bioinformatics/btp352
PubMed ID
19505943
PubMed Central ID
PMC2723002
Links
Grant list
U54HG002750 / 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

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