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
  • [31] De novo RNA-Seq and functional annotation of Sarcoptes scabiei canis
    Li Hu
    YaE Zhao
    YuanJun Yang
    DongLing Niu
    RuiLing Wang
    Juan Cheng
    Fan Yang
    Parasitology Research, 2016, 115 : 2661 - 2670
  • [32] Differentially Expressed Genes in Hypericin-Containing Hypericum perforatum Leaf Tissues as Revealed by De Novo Assembly of RNA-Seq
    Miroslav Soták
    Odeta Czeranková
    Daniel Klein
    Katarína Nigutová
    Lothar Altschmied
    Ling Li
    Adarsch Jose
    Eve Syrkin Wurtele
    Eva Čellárová
    Plant Molecular Biology Reporter, 2016, 34 : 1027 - 1041
  • [33] RNA-Seq De Novo Assembly of Red Pitaya (Hylocereus polyrhizus) Roots and Differential Transcriptome Analysis in Response to Salt Stress
    Nong, Quandong
    Zhang, Mingyong
    Chen, Jiantong
    Zhang, Mei
    Cheng, Huaping
    Jian, Shuguang
    Lu, Hongfang
    Xia, Kuaifei
    TROPICAL PLANT BIOLOGY, 2019, 12 (02) : 55 - 66
  • [34] RNA-Seq De Novo Assembly of Red Pitaya (Hylocereus polyrhizus) Roots and Differential Transcriptome Analysis in Response to Salt Stress
    Quandong Nong
    Mingyong Zhang
    Jiantong Chen
    Mei Zhang
    Huaping Cheng
    Shuguang Jian
    Hongfang Lu
    Kuaifei Xia
    Tropical Plant Biology, 2019, 12 : 55 - 66
  • [35] Differentially Expressed Genes in Hypericin-Containing Hypericum perforatum Leaf Tissues as Revealed by De Novo Assembly of RNA-Seq
    Sotak, Miroslav
    Czerankova, Odeta
    Klein, Daniel
    Nigutova, Katarina
    Altschmied, Lothar
    Li, Ling
    Jose, Adarsch
    Wurtele, Eve Syrkin
    Cellarova, Eva
    PLANT MOLECULAR BIOLOGY REPORTER, 2016, 34 (05) : 1027 - 1041
  • [36] SSP: An interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads
    Safikhani, Zhaleh
    Sadeghi, Mehdi
    Pezeshk, Hamid
    Eslahchi, Changiz
    GENOMICS, 2013, 102 (5-6) : 507 - 514
  • [37] Optimizing RNA-seq studies to investigate herbicide resistance
    Giacomini, Darci A.
    Gaines, Todd
    Beffa, Roland
    Tranel, Patrick J.
    PEST MANAGEMENT SCIENCE, 2018, 74 (10) : 2260 - 2264
  • [38] De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis
    Bai, Chengke
    Wu, Yongmei
    Cao, Bo
    Xu, Jun
    Li, Guishuang
    TREE GENETICS & GENOMES, 2018, 14 (04)
  • [39] The Utility of Data Transformation for Alignment, De Novo Assembly and Classification of Short Read Virus Sequences
    Tapinos, Avraam
    Constantinides, Bede
    Phan, My V. T.
    Kouchaki, Samaneh
    Cotten, Matthew
    Robertson, David L.
    VIRUSES-BASEL, 2019, 11 (05):
  • [40] De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis
    Chengke Bai
    Yongmei Wu
    Bo Cao
    Jun Xu
    Guishuang Li
    Tree Genetics & Genomes, 2018, 14