Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

被引：0
|
作者：
Rob Patro
Stephen M Mount
Carl Kingsford
机构：
[1] Lane Center for Computational Biology,Department of Cell Biology and Molecular Genetics
[2] School of Computer Science,undefined
[3] Carnegie Mellon University,undefined
[4] University of Maryland,undefined
[5] Center for Bioinformatics and Computational Biology,undefined
[6] University of Maryland,undefined
来源：
Nature Biotechnology | 2014年 / 32卷
关键词：
D O I：
暂无
中图分类号：
学科分类号：
摘要：
A new algorithm speeds up the quantification of transcripts from RNA-seq data by doing away with read mapping.
引用
收藏
页码：462 / 464
页数：2
相关论文
共 30 条
  • [1] Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
    Patro, Rob
    Mount, Stephen M.
    Kingsford, Carl
    NATURE BIOTECHNOLOGY, 2014, 32 (05) : 462 - U174
  • [2] Limitations of alignment-free tools in total RNA-seq quantification
    Douglas C. Wu
    Jun Yao
    Kevin S. Ho
    Alan M. Lambowitz
    Claus O. Wilke
    BMC Genomics, 19
  • [3] Limitations of alignment-free tools in total RNA-seq quantification
    Wu, Douglas C.
    Yao, Jun
    Ho, Kevin S.
    Lambowitz, Alanm.
    Wilke, Claus O.
    BMC GENOMICS, 2018, 19
  • [4] Simultaneous Isoform Discovery and Quantification from RNA-Seq
    Hiller D.
    Wong W.H.
    Statistics in Biosciences, 2013, 5 (1) : 100 - 118
  • [5] StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
    Mihaela Pertea
    Geo M Pertea
    Corina M Antonescu
    Tsung-Cheng Chang
    Joshua T Mendell
    Steven L Salzberg
    Nature Biotechnology, 2015, 33 : 290 - 295
  • [6] StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
    Pertea, Mihaela
    Pertea, Geo M.
    Antonescu, Corina M.
    Chang, Tsung-Cheng
    Mendell, Joshua T.
    Salzberg, Steven L.
    NATURE BIOTECHNOLOGY, 2015, 33 (03) : 290 - +
  • [7] Towards Reliable Isoform Quantification Using RNA-Seq Data
    Howard, Brian E.
    Heber, Steffen
    2009 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, 2009, : 130 - 135
  • [8] Towards reliable isoform quantification using RNA-SEQ data
    Brian E Howard
    Steffen Heber
    BMC Bioinformatics, 11
  • [9] Towards reliable isoform quantification using RNA-SEQ data
    Howard, Brian E.
    Heber, Steffen
    BMC BIOINFORMATICS, 2010, 11
  • [10] An Alignment-Free Regression Approach for Estimating Allele-Specific Expression Using RNA-Seq Data
    Fu, Chen-Ping
    Jojic, Vladimir
    McMillan, Leonard
    RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, RECOMB2014, 2014, 8394 : 69 - 84
123