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
  • [41] De novo assembly and characterisation of the field pea transcriptome using RNA-Seq
    Shimna Sudheesh
    Timothy I. Sawbridge
    Noel OI Cogan
    Peter Kennedy
    John W. Forster
    Sukhjiwan Kaur
    BMC Genomics, 16
  • [42] De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy
    Farrell, Jacqueline D.
    Byrne, Stephen
    Paina, Cristiana
    Asp, Torben
    PLOS ONE, 2014, 9 (08):
  • [43] Evaluation of de novo transcriptome assemblies from RNA-Seq data
    Li, Bo
    Fillmore, Nathanael
    Bai, Yongsheng
    Collins, Mike
    Thomson, James A.
    Stewart, Ron
    Dewey, Colin N.
    GENOME BIOLOGY, 2014, 15 (12):
  • [44] On de novo Bridging Paired-end RNA-seq Data
    Li, Xiang
    Shao, Mingfu
    14TH ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY, AND HEALTH INFORMATICS, BCB 2023, 2023,
  • [45] Evaluation of de novo transcriptome assemblies from RNA-Seq data
    Bo Li
    Nathanael Fillmore
    Yongsheng Bai
    Mike Collins
    James A Thomson
    Ron Stewart
    Colin N Dewey
    Genome Biology, 15
  • [46] Utilizing RNA-Seq data for de novo coexpression network inference
    Iancu, Ovidiu D.
    Kawane, Sunita
    Bottomly, Daniel
    Searles, Robert
    Hitzemann, Robert
    McWeeney, Shannon
    BIOINFORMATICS, 2012, 28 (12) : 1592 - 1597
  • [47] Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
    Leandro Lima
    Blerina Sinaimeri
    Gustavo Sacomoto
    Helene Lopez-Maestre
    Camille Marchet
    Vincent Miele
    Marie-France Sagot
    Vincent Lacroix
    Algorithms for Molecular Biology, 12
  • [48] Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads
    Lima, Leandro
    Sinaimeri, Blerina
    Sacomoto, Gustavo
    Lopez-Maestre, Helene
    Marchet, Camille
    Miele, Vincent
    Sagot, Marie-France
    Lacroix, Vincent
    ALGORITHMS FOR MOLECULAR BIOLOGY, 2017, 12
  • [49] SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
    Dohm, Juliane C.
    Lottaz, Claudio
    Borodina, Tatiana
    Himmelbauer, Heinz
    GENOME RESEARCH, 2007, 17 (11) : 1697 - 1706
  • [50] De novo transcriptome assembly of the Chinese pearl barley, adlay, by full-length isoform and short-read RNA sequencing
    Kang, Sang-Ho
    Lee, Jong-Yeol
    Lee, Tae-Ho
    Park, Soo-Yun
    Kim, Chang-Kug
    PLOS ONE, 2018, 13 (12):
12345