mrsFAST: a cache-oblivious algorithm for short-read mapping

被引:189
作者
Hach, Faraz [1 ]
Hormozdiari, Fereydoun [1 ]
Alkan, Can [2 ,3 ]
Hormozdiari, Farhad [1 ]
Birol, Inanc [1 ,4 ]
Eichler, Evan E. [2 ,3 ]
Sahinalp, S. Cenk [1 ,2 ]
机构
[1] Simon Fraser Univ, Sch Comp Sci, Burnaby, BC V5A 1S6, Canada
[2] Univ Washington, Sch Med, Dept Genom, Seattle, WA USA
[3] Howard Hughes Med Inst, Seattle, WA USA
[4] British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
关键词
ALIGNMENT;
D O I
10.1038/nmeth0810-576
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
引用
收藏
页码:576 / 577
页数:3
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共 7 条
[1]   Personalized copy number and segmental duplication maps using next-generation sequencing [J].
Alkan, Can ;
Kidd, Jeffrey M. ;
Marques-Bonet, Tomas ;
Aksay, Gozde ;
Antonacci, Francesca ;
Hormozdiari, Fereydoun ;
Kitzman, Jacob O. ;
Baker, Carl ;
Malig, Maika ;
Mutlu, Onur ;
Sahinalp, S. Cenk ;
Gibbs, Richard A. ;
Eichler, Evan E. .
NATURE GENETICS, 2009, 41 (10) :1061-U29
[2]   Opportunistic data structures with applications [J].
Ferragina, P ;
Manzini, G .
41ST ANNUAL SYMPOSIUM ON FOUNDATIONS OF COMPUTER SCIENCE, PROCEEDINGS, 2000, :390-398
[3]   Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes [J].
Hormozdiari, Fereydoun ;
Alkan, Can ;
Eichler, Evan E. ;
Sahinalp, S. Cenk .
GENOME RESEARCH, 2009, 19 (07) :1270-1278
[4]   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)
[5]   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
[6]   Fast and accurate short read alignment with Burrows-Wheeler transform [J].
Li, Heng ;
Durbin, Richard .
BIOINFORMATICS, 2009, 25 (14) :1754-1760
[7]   RazerS-fast read mapping with sensitivity control [J].
Weese, David ;
Emde, Anne-Katrin ;
Rausch, Tobias ;
Doering, Andreas ;
Reinert, Knut .
GENOME RESEARCH, 2009, 19 (09) :1646-1654