How to map billions of short reads onto genomes

被引:175
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
    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
    [J]. GENOME BIOLOGY, 2008, 9 (12)
  • [2] Genome-wide mapping of in vivo protein-DNA interactions
    Johnson, David S.
    Mortazavi, Ali
    Myers, Richard M.
    Wold, Barbara
    [J]. SCIENCE, 2007, 316 (5830) : 1497 - 1502
  • [3] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Langmead, Ben
    Trapnell, Cole
    Pop, Mihai
    Salzberg, Steven L.
    [J]. GENOME BIOLOGY, 2009, 10 (03):
  • [4] The first human acute myeloid leukemia genome ever fully sequenced
    Falini, Brunangelo
    [J]. HAEMATOLOGICA, 2024, 109 (01) : 1 - 2
  • [5] Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Li, Heng
    Ruan, Jue
    Durbin, Richard
    [J]. GENOME RESEARCH, 2008, 18 (11) : 1851 - 1858
  • [6] Mapping and quantifying mammalian transcriptomes by RNA-Seq
    Mortazavi, Ali
    Williams, Brian A.
    McCue, Kenneth
    Schaeffer, Lorian
    Wold, Barbara
    [J]. NATURE METHODS, 2008, 5 (07) : 621 - 628
  • [7] The transcriptional landscape of the yeast genome defined by RNA sequencing
    Nagalakshmi, Ugrappa
    Wang, Zhong
    Waern, Karl
    Shou, Chong
    Raha, Debasish
    Gerstein, Mark
    Snyder, Michael
    [J]. SCIENCE, 2008, 320 (5881) : 1344 - 1349
  • [8] Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    Pan, Qun
    Shai, Ofer
    Lee, Leo J.
    Frey, J.
    Blencowe, Benjamin J.
    [J]. NATURE GENETICS, 2008, 40 (12) : 1413 - 1415
  • [9] TopHat: discovering splice junctions with RNA-Seq
    Trapnell, Cole
    Pachter, Lior
    Salzberg, Steven L.
    [J]. BIOINFORMATICS, 2009, 25 (09) : 1105 - 1111
  • [10] Alternative isoform regulation in human tissue transcriptomes
    Wang, Eric T.
    Sandberg, Rickard
    Luo, Shujun
    Khrebtukova, Irina
    Zhang, Lu
    Mayr, Christine
    Kingsmore, Stephen F.
    Schroth, Gary P.
    Burge, Christopher B.
    [J]. NATURE, 2008, 456 (7221) : 470 - 476