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

Xie, Yinlong, Wu, Gengxiong, Tang, Jingbo, Luo, Ruibang, Patterson, Jordan, Liu, Shanlin, Huang, Weihua, He, Guangzhu, Gu, Shengchang, Li, Shengkang, Zhou, Xin, Lam, Tak-Wah, Li, Yingrui, Xu, Xun, Wong, Gane Ka-Shu and Wang, Jun (2014) SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads. Bioinformatics, 30 12: 1660-1666. doi:10.1093/bioinformatics/btu077

Author Xie, Yinlong
Wu, Gengxiong
Tang, Jingbo
Luo, Ruibang
Patterson, Jordan
Liu, Shanlin
Huang, Weihua
He, Guangzhu
Gu, Shengchang
Li, Shengkang
Zhou, Xin
Lam, Tak-Wah
Li, Yingrui
Xu, Xun
Wong, Gane Ka-Shu
Wang, Jun
Title SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-Seq reads
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1460-2059
Publication date 2014-02-13
Year available 2014
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btu077
Open Access Status DOI
Volume 30
Issue 12
Start page 1660
End page 1666
Total pages 7
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Formatted abstract
Motivation: 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.
Results: Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
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