How to map billions of short reads onto genomes

被引:176
作者
Trapnell, Cole [1 ]
Salzberg, Steven L. [1 ]
机构
[1] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA
关键词
D O I
10.1038/nbt0509-455
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Mapping the vast quantities of short sequence fragments produced by next-generation sequencing platforms is a challenge. What programs are available and how do they work?
引用
收藏
页码:455 / 457
页数:3
相关论文
共 10 条
[1]   Annotating genomes with massive-scale RNA sequencing [J].
Denoeud, France ;
Aury, Jean-Marc ;
Da Silva, Corinne ;
Noel, Benjamin ;
Rogier, Odile ;
Delledonne, Massimo ;
Morgante, Michele ;
Valle, Giorgio ;
Wincker, Patrick ;
Scarpelli, Claude ;
Jaillon, Olivier ;
Artiguenave, Francois .
GENOME BIOLOGY, 2008, 9 (12)
[2]   Genome-wide mapping of in vivo protein-DNA interactions [J].
Johnson, David S. ;
Mortazavi, Ali ;
Myers, Richard M. ;
Wold, Barbara .
SCIENCE, 2007, 316 (5830) :1497-1502
[3]   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)
[4]  
Ley TJ, 2008, NATURE, V456, P66, DOI 10.1038/nature07485
[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]   Mapping and quantifying mammalian transcriptomes by RNA-Seq [J].
Mortazavi, Ali ;
Williams, Brian A. ;
McCue, Kenneth ;
Schaeffer, Lorian ;
Wold, Barbara .
NATURE METHODS, 2008, 5 (07) :621-628
[7]   The transcriptional landscape of the yeast genome defined by RNA sequencing [J].
Nagalakshmi, Ugrappa ;
Wang, Zhong ;
Waern, Karl ;
Shou, Chong ;
Raha, Debasish ;
Gerstein, Mark ;
Snyder, Michael .
SCIENCE, 2008, 320 (5881) :1344-1349
[8]   Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing [J].
Pan, Qun ;
Shai, Ofer ;
Lee, Leo J. ;
Frey, J. ;
Blencowe, Benjamin J. .
NATURE GENETICS, 2008, 40 (12) :1413-1415
[9]   TopHat: discovering splice junctions with RNA-Seq [J].
Trapnell, Cole ;
Pachter, Lior ;
Salzberg, Steven L. .
BIOINFORMATICS, 2009, 25 (09) :1105-1111
[10]   Alternative isoform regulation in human tissue transcriptomes [J].
Wang, Eric T. ;
Sandberg, Rickard ;
Luo, Shujun ;
Khrebtukova, Irina ;
Zhang, Lu ;
Mayr, Christine ;
Kingsmore, Stephen F. ;
Schroth, Gary P. ;
Burge, Christopher B. .
NATURE, 2008, 456 (7221) :470-476