title: OSA: a fast and accurate alignment tool for RNA-Seq.
abstract: Accurately mapping RNA-Seq reads to the reference genome is a critical step for performing downstream analysis such as transcript assembly, isoform detection and quantification. Many tools have been developed; however, given the huge size of the next generation sequencing datasets and the complexity of the transcriptome, RNA-Seq read mapping remains a challenge with the ever-increasing amount of data. We develop Omicsoft sequence aligner (OSA), a fast and accurate alignment tool for RNA-Seq data. Benchmarked with existing methods, OSA improves mapping speed 4-10-fold with better sensitivity and less false positives.
  
  
  BACKGROUND
  OSA can be downloaded from http://omicsoft.com/osa. It is free to academic users. OSA has been tested extensively on Linux, Mac OS X and Windows platforms.
authors.affiliation: Division of Bioinformatics, Omicsoft Inc., 164 Quade Drive, Cary, NC 27513, USA. john.hu@omicsoft.com
authors.forename: Jun
authors.initials: J
authors.lastname: Hu
authors.forename: Huanying
authors.initials: H
authors.lastname: Ge
authors.forename: Matt
authors.initials: M
authors.lastname: Newman
authors.forename: Kejun
authors.initials: K
authors.lastname: Liu
mesh_terms: D019295:Computational Biology / Q000379:methods; D016678:Genome; D012313:RNA / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
chemical_list: D012313:RNA