Journal
BIOINFORMATICS
Volume 30, Issue 12, Pages 1660-1666Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu077
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Funding
- State Key Development Program for Basic Research of China-973 Program [2011CB809202]
- Shenzhen Key Laboratory of Transomics Biotechnologies [CXB201108250096A]
- China National GeneBank
- 1000 plants (1KP) initiative - Alberta Ministry of Enterprise and Advanced Education
- Alberta Innovates Technology Futures (AITF) Innovates Centre of Research Excellence: (iCORE)
- Musea Ventures
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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 x 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.
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