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

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. 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. Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/.

Xie Y ，Wu G ，Tang J ，Luo R ，Patterson J ，Liu S ，Huang W ，He G ，Gu S ，Li S ，Zhou X ，Lam TW ，Li Y ，Xu X ，Wong GK ，Wang J ... -  《-》

Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis.

Wang S ，Gribskov M 《-》

A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing.

Hoang NV ，Furtado A ，Mason PJ ，Marquardt A ，Kasirajan L ，Thirugnanasambandam PP ，Botha FC ，Henry RJ ... -  《BMC GENOMICS》

Comparison of De Novo Transcriptome Assemblers and k-mer Strategies Using the Killifish, Fundulus heteroclitus.

Rana SB ，Zadlock FJ 4th ，Zhang Z ，Murphy WR ，Bentivegna CS ... -  《PLoS One》

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.

Chang Z ，Li G ，Liu J ，Zhang Y ，Ashby C ，Liu D ，Cramer CL ，Huang X ... -  《GENOME BIOLOGY》