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

Motivation: Transcriptomesequencing 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-Seqin 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 assemblerdesigned specifically for RNA-Seq. We evaluated its performance on transcriptomedatasets from rice and mouse. Using as our benchmarks the known transcripts from these wellannotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptomeassemblers 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.