SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads | Zendy

Yinlong Xie | Zendy; Gengxiong Wu | Zendy; Jingbo Tang | Zendy; Ruibang Luo | Zendy; Jordan Patterson | Zendy; Shanlin Liu | Zendy; Weihua Huang | Zendy; Guangzhu He | Zendy; Shengchang Gu | Zendy; Shengkang Li | Zendy; Xin Zhou | Zendy; TakWah Lam | Zendy; Yingrui Li | Zendy; Xun Xu | Zendy; Gane KaShu Wong | Zendy; Jun Wang | Zendy

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SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

Author(s) -

Yinlong Xie,

Gengxiong Wu,

Jingbo Tang,

Ruibang Luo,

Jordan Patterson,

Shanlin Liu,

Weihua Huang,

Guangzhu He,

Shengchang Gu,

Shengkang Li,

Xin Zhou,

TakWah Lam,

Yingrui Li,

Xun Xu,

Gane KaShu Wong,

Jun Wang

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu077

Subject(s) - transcriptome , de novo transcriptome assembly , rna seq , sequence assembly , computational biology , biology , genome , redundancy (engineering) , dna sequencing , gene , alternative splicing , reference genome , rna , computer science , genetics , messenger rna , gene expression , operating system

Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge.

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