De novo assembly of bacterial transcriptomes from RNA-seq data

Transcriptome assays are increasingly being performed by high- throughput RNA sequencing ( RNA- seq). For organisms whose genomes have not been sequenced and annotated, transcriptomes must be assembled de novo from the RNA- seq data. Here, we present novel algorithms, specific to bacterial gene structures and transcriptomes, for analysis of bacterial RNA- seq data and de novo transcriptome assembly. The algorithms are implemented in an open source software system called Rockhopper 2. We find that Rockhopper 2 outperforms other de novo transcriptome assemblers and offers accurate and efficient analysis of bacterial RNA- seq data. Rockhopper 2 is available at http:// cs. wellesley. edu/similar to btjaden/ Rockhopper.