De novo assembly of bacterial transcriptomes from RNA-seq data

TLDR

RNA‑seq is increasingly used for transcriptome assays, but for organisms without sequenced genomes, de novo assembly is required. The study introduces novel bacterial‑specific algorithms for de novo transcriptome assembly and RNA‑seq analysis. These algorithms are implemented in the open‑source Rockhopper 2 software. Rockhopper 2 outperforms other de novo assemblers, providing accurate and efficient bacterial RNA‑seq analysis. Rockhopper 2 is available at http://cs.wellesley.edu/~btjaden/Rockhopper.

Abstract

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/~btjaden/Rockhopper .