General Information
| Description | De novo transcriptome assembly with short RNA-Seq reads |
| Homepage | http://sourceforge.net/projects/soapdenovotrans/ |
Publications
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
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 http://sourceforge.net/projects/soapdenovotrans/.
Contact:
xieyl@genomics.cn or bgi-soap@googlegroups.com
Supplementary information:
Supplementary data are available at Bioinformatics online.
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