title: De novo assembly of bacterial transcriptomes from RNA-seq data.
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 .
authors.affiliation: Computer Science Department, Wellesley College, Wellesley, MA, 02481, USA. btjaden@wellesley.edu.
authors.forename: Brian
authors.initials: B
authors.lastname: Tjaden
mesh_terms: D001419:Bacteria / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D030561:Databases, Nucleic Acid; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D012329:RNA, Bacterial / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D012329:RNA, Bacterial; D012333:RNA, Messenger