Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

被引:0
|
作者
Ya Yang
Stephen A Smith
机构
[1] University of Michigan,Department of Ecology & Evolutionary Biology
来源
BMC Genomics | / 14卷
关键词
1KP; Chimera; assembly; Redundancy; RNA-seq; SOAPdenovo-Trans; Trans-ABySS; Transcriptome; Trinity; Oases;
D O I
暂无
中图分类号
学科分类号
摘要
引用
收藏
相关论文
共 50 条
  • [1] Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
    Yang, Ya
    Smith, Stephen A.
    BMC GENOMICS, 2013, 14
  • [2] Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data
    Duan, Jialei
    Xia, Chuan
    Zhao, Guangyao
    Jia, Jizeng
    Kong, Xiuying
    BMC GENOMICS, 2012, 13
  • [3] Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data
    Jialei Duan
    Chuan Xia
    Guangyao Zhao
    Jizeng Jia
    Xiuying Kong
    BMC Genomics, 13
  • [4] Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
    Zhao, Qiong-Yi
    Wang, Yi
    Kong, Yi-Meng
    Luo, Da
    Li, Xuan
    Hao, Pei
    BMC BIOINFORMATICS, 2011, 12 : S2
  • [5] Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
    Qiong-Yi Zhao
    Yi Wang
    Yi-Meng Kong
    Da Luo
    Xuan Li
    Pei Hao
    BMC Bioinformatics, 12
  • [6] De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
    Hoelzer, Martin
    Marz, Manja
    GIGASCIENCE, 2019, 8 (05):
  • [7] NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data
    Overbey, Eliah G.
    Saravia-Butler, Amanda M.
    Zhang, Zhe
    Rathi, Komal S.
    Fogle, Homer
    da Silveira, Willian A.
    Barker, Richard J.
    Bass, Joseph J.
    Beheshti, Afshin
    Berrios, Daniel C.
    Blaber, Elizabeth A.
    Cekanaviciute, Egle
    Costa, Helio A.
    Davin, Laurence B.
    Fisch, Kathleen M.
    Gebre, Samrawit G.
    Geniza, Matthew
    Gilbert, Rachel
    Gilroy, Simon
    Hardiman, Gary
    Herranz, Raul
    Kidane, Yared H.
    Kruse, Colin P. S.
    Lee, Michael D.
    Liefeld, Ted
    Lewis, Norman G.
    McDonald, J. Tyson
    Meller, Robert
    Mishra, Tejaswini
    Perera, Imara Y.
    Ray, Shayoni
    Reinsch, Sigrid S.
    Rosenthal, Sara Brin
    Strong, Michael
    Szewczyk, Nathaniel J.
    Tahimic, Candice G. T.
    Taylor, Deanne M.
    Vandenbrink, Joshua P.
    Villacampa, Alicia
    Weging, Silvio
    Wolverton, Chris
    Wyatt, Sarah E.
    Zea, Luis
    Costes, Sylvain, V
    Galazka, Jonathan M.
    ISCIENCE, 2021, 24 (04)
  • [8] De novo assembly and analysis of RNA-seq data
    Robertson, Gordon
    Schein, Jacqueline
    Chiu, Readman
    Corbett, Richard
    Field, Matthew
    Jackman, Shaun D.
    Mungall, Karen
    Lee, Sam
    Okada, Hisanaga Mark
    Qian, Jenny Q.
    Griffith, Malachi
    Raymond, Anthony
    Thiessen, Nina
    Cezard, Timothee
    Butterfield, Yaron S.
    Newsome, Richard
    Chan, Simon K.
    She, Rong
    Varhol, Richard
    Kamoh, Baljit
    Prabhu, Anna-Liisa
    Tam, Angela
    Zhao, YongJun
    Moore, Richard A.
    Hirst, Martin
    Marra, Marco A.
    Jones, Steven J. M.
    Hoodless, Pamela A.
    Birol, Inanc
    NATURE METHODS, 2010, 7 (11) : 909 - U62
  • [9] De novo assembly and analysis of RNA-seq data
    Gordon Robertson
    Jacqueline Schein
    Readman Chiu
    Richard Corbett
    Matthew Field
    Shaun D Jackman
    Karen Mungall
    Sam Lee
    Hisanaga Mark Okada
    Jenny Q Qian
    Malachi Griffith
    Anthony Raymond
    Nina Thiessen
    Timothee Cezard
    Yaron S Butterfield
    Richard Newsome
    Simon K Chan
    Rong She
    Richard Varhol
    Baljit Kamoh
    Anna-Liisa Prabhu
    Angela Tam
    YongJun Zhao
    Richard A Moore
    Martin Hirst
    Marco A Marra
    Steven J M Jones
    Pamela A Hoodless
    Inanc Birol
    Nature Methods, 2010, 7 : 909 - 912
  • [10] Modeling non-uniformity in short-read rates in RNA-Seq data
    Li, Jun
    Jiang, Hui
    Wong, Wing Hung
    GENOME BIOLOGY, 2010, 11 (05):