De novo assembly of bacterial transcriptomes from RNA-seq data

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


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 .

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Bacteria / genetics*
  • DNA, Bacterial / genetics
  • Databases, Nucleic Acid*
  • Gene Expression Regulation, Bacterial
  • Genome, Bacterial
  • RNA, Bacterial / genetics*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA / methods*
  • Software
  • Transcriptome / genetics*


  • DNA, Bacterial
  • RNA, Bacterial
  • RNA, Messenger