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

Published on Jun 15, 2014in Bioinformatics4.53
· DOI :10.1093/bioinformatics/btu077
Yinlong Xie6
Estimated H-index: 6
(SCUT: South China University of Technology),
Gengxiong Wu5
Estimated H-index: 5
+ 13 AuthorsJun Wang141
Estimated H-index: 141
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 wellannotated 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 Contact: or Supplementary information: Supplementary data are available at Bioinformatics online.
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