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PMID: 19505943 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

The Sequence Alignment/Map format and SAMtools.

Bioinformatics (Oxford, England) ·Vol. 25 ·No. 16 ·2009-08-15 ·Pages 2078-9

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup

Abstract

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. http://samtools.sourceforge.net.

MeSH Terms
Algorithms Base Sequence Computational Biology/methods Genome Genomics Molecular Sequence Data Sequence Alignment/methods Sequence Analysis, DNA/methods Software
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Li Heng
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
Handsaker Bob
Wysoker Alec
Fennell Tim
Ruan Jue
Homer Nils
Marth Gabor
Abecasis Goncalo
Durbin Richard
1000 Genome Project Data Processing Subgroup
References (4)
4 references, click to expand
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  2. Next-generation DNA sequencing methods.
    Annu Rev Genomics Hum Genet. 2008;9:387-402 PMID: 18576944
  3. Mapping short DNA sequencing reads and calling variants using mapping quality scores.
    Genome Res. 2008 Nov;18(11):1851-8 PMID: 18714091
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    Genome Biol. 2009;10(3):R25 PMID: 19261174
Article Info
Journal
Bioinformatics (Oxford, England)
Abbr.
Bioinformatics
ISSN
1367-4811
DOI
10.1093/bioinformatics/btp352
Published
2009-08-15
Epub
2009-00-08
Pages
2078-9
Language
English
Region
England
NLM ID
9808944
PMCID
PMC2723002
Subset
IM
Grants
NHGRI NIH HHS · U54HG002750 · United States
NHGRI NIH HHS · R01 HG004719-01 · United States
NHGRI NIH HHS · U54 HG002750 · United States
Wellcome Trust · 077192/Z/05/Z · United Kingdom
NHGRI NIH HHS · R01 HG004719-02 · United States
NHGRI NIH HHS · R01 HG004719 · United States
NHGRI NIH HHS · R01 HG004719-04 · United States
NHGRI NIH HHS · R01 HG004719-02S1 · United States
NHGRI NIH HHS · R01 HG004719-03 · United States
External Links
PubMed source DOI: 10.1093/bioinformatics/btp352 PMC Full Text View journal details
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