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

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
Bioinformatics 2014 June 15, 30 (12): 1660-6

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

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