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

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ID: 301430
2014
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Abstract
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. Availability and implementation: Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/. Contact: xieyl@genomics.cn or bgi-soap@googlegroups.com Supplementary information: Supplementary data are available at Bioinformatics online.
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Authors Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Shengkang Li, Xin Zhou, Tak‐Wah Lam, Yingrui Li, Xun Xu, Gane Ka‐Shu Wong, Jun Wang
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Journal BMC Bioinformatics
Year 2014
DOI
10.1093/bioinformatics/btu077
URL
https://academic.oup.com/bioinformatics/article-pdf/30/12/1660/48927094/bioinformatics_30_12_1660.pdf
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