title: Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
abstract: BACKGROUND
  Comprehensive annotation and quantification of transcriptomes are outstanding problems in functional genomics. While high throughput mRNA sequencing (RNA-Seq) has emerged as a powerful tool for addressing these problems, its success is dependent upon the availability and quality of reference genome sequences, thus limiting the organisms to which it can be applied.
  
  
  RESULTS
  Here, we describe Rnnotator, an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome. We have applied the Rnnotator assembly pipeline to two yeast transcriptomes and compared the results to the reference gene catalogs of these organisms. The contigs produced by Rnnotator are highly accurate (95%) and reconstruct full-length genes for the majority of the existing gene models (54.3%). Furthermore, our analyses revealed many novel transcribed regions that are absent from well annotated genomes, suggesting Rnnotator serves as a complementary approach to analysis based on a reference genome for comprehensive transcriptomics.
  
  
  CONCLUSIONS
  These results demonstrate that the Rnnotator pipeline is able to reconstruct full-length transcripts in the absence of a complete reference genome.
authors.affiliation: Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Martin
authors.forename: Vincent M
authors.initials: VM
authors.lastname: Bruno
authors.forename: Zhide
authors.initials: Z
authors.lastname: Fang
authors.forename: Xiandong
authors.initials: X
authors.lastname: Meng
authors.forename: Matthew
authors.initials: M
authors.lastname: Blow
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.forename: Gavin
authors.initials: G
authors.lastname: Sherlock
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
mesh_terms: D001331:Automation; D001483:Base Sequence; D002176:Candida albicans / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger