  Motivation: Transcriptome sequencing has long been the favored method for
quickly and inexpensively obtaining the sequences for a large number of genes
from an organism with no reference genome. With the rapidly increasing
throughputs and decreasing costs of next generation sequencing, RNA-Seq has
gained in popularity; but given the typically short reads (e.g. 2 x 90 bp
paired ends) of this technol- ogy, de novo assembly to recover complete or
full-length transcript sequences remains an algorithmic challenge. Results: We
present SOAPdenovo-Trans, a de novo transcriptome assembler designed
specifically for RNA-Seq. Its performance was evaluated on transcriptome
datasets from rice and mouse. Using the known transcripts from these
well-annotated genomes (sequenced a decade ago) as our benchmark, we assessed
how SOAPdenovo- Trans and two other popular software handle the practical
issues of 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 at http://sourceforge.net/projects/soapdenovotrans/ Contact:
<EMAIL_ADDRESS>or<EMAIL_ADDRESS>