De novo assembly of bacterial transcriptomes from RNA-seq data

By Brian Tjaden. Genome Biology, 2015

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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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a891e2ec28a14a1ef5d13c03daf9c8ea0dd97953