The Sequence Alignment/Map format and SAMtools

被引：19515

作者：

Li, Heng ^{[1
]}

Handsaker, Bob ^{[2
,3
]}

Wysoker, Alec ^{[2
,3
]}

Fennell, Tim ^{[2
,3
]}

Ruan, Jue ^{[4
]}

Homer, Nils ^{[5
]}

Marth, Gabor ^{[6
]}

Abecasis, Goncalo ^{[7
]}

Durbin, Richard ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] MIT, Broad Inst, Cambridge, MA 02141 USA

[3] Broad Inst MIT & Harvard, Cambridge, MA 02141 USA

[4] Chinese Acad Sci, Beijing Inst Genom, Beijing 100029, Peoples R China

[5] Univ Calif Los Angeles, Dept Comp Sci, Los Angeles, CA 90095 USA

[6] Boston Coll, Dept Biol, Chestnut Hill, MA 02467 USA

[7] Univ Michigan, Dept Biostat, Ctr Stat Genet, Ann Arbor, MI 48109 USA

来源：

BIOINFORMATICS | 2009年 / 25卷 / 16期

基金：

英国惠康基金;

关键词：

HUMAN GENOME;

D O I：

10.1093/bioinformatics/btp352

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2078 / 2079

页数：2

共 4 条

[1] The human genome browser at UCSC [J].

Kent, WJ ;

Sugnet, CW ;

Furey, TS ;

Roskin, KM ;

Pringle, TH ;

Zahler, AM ;

Haussler, D .

GENOME RESEARCH, 2002, 12 (06) :996-1006

[2] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome [J].

Langmead, Ben ;

Trapnell, Cole ;

Pop, Mihai ;

Salzberg, Steven L. .

GENOME BIOLOGY, 2009, 10 (03)

[3] Mapping short DNA sequencing reads and calling variants using mapping quality scores [J].

Li, Heng ;

Ruan, Jue ;

Durbin, Richard .

GENOME RESEARCH, 2008, 18 (11) :1851-1858

[4] Next-generation DNA sequencing methods [J].

Mardis, Elaine R. .

ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2008, 9 :387-402

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