title: Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels.
abstract: BACKGROUND
  High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values.
  
  
  RESULTS
  We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.
  
  
  METHODS
  Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/.
authors.affiliation: Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
authors.forename: Marcel H
authors.initials: MH
authors.lastname: Schulz
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Zerbino
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
authors.forename: Ewan
authors.initials: E
authors.lastname: Birney
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D000818:Animals; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012333:RNA, Messenger