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

• Published in: Bioinformatics (Oxford, England) England), 2014-06, Vol.30 (12), p.1660-1666
• Main Authors: 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
• Format: Article
• Language: English
• Subjects: Algorithms; Alternative Splicing; Animals; Gene Expression Profiling - methods; Genomics - methods; High-Throughput Nucleotide Sequencing - methods; Mice; Oryza - genetics; Sequence Analysis, RNA - methods
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btu077

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. 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. Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/.