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Genome Biol. 2015 Jan 13;16:1. doi: 10.1186/s13059-014-0572-2.

De novo assembly of bacterial transcriptomes from RNA-seq data.

Author information

1
Computer Science Department, Wellesley College, Wellesley, MA, 02481, USA. btjaden@wellesley.edu.

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 .

PMID:
25583448
PMCID:
PMC4316799
DOI:
10.1186/s13059-014-0572-2
[Indexed for MEDLINE]
Free PMC Article

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