title: EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.
abstract: BACKGROUND
  High-accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. We introduce a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm uses an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data.
  
  
  RESULTS
  EBARDenovo resolves the complications of RNA-Seq assembly arising from sequencing errors, repetitive sequences and aberrant chimeric amplicons. In a series of assembly experiments, our algorithm is the most accurate among the examined programs, including de Bruijn graph assemblers, Trinity and Oases.
  
  
  METHODS
  EBARDenovo is available at http://ebardenovo.sourceforge.net/. This software package (with patent pending) is free of charge for academic use only.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Biomedical informatics, Department of Computer Science and Information Engineering, Asia University, Taichung, Taiwan. htchu@asia.edu.tw
authors: Hsueh-Ting
authors: HT
authors: Chu
authors: William W L
authors: WW
authors: Hsiao
authors: Jen-Chih
authors: JC
authors: Chen
authors: Tze-Jung
authors: TJ
authors: Yeh
authors: Mong-Hsun
authors: MH
authors: Tsai
authors: Han
authors: H
authors: Lin
authors: Yen-Wenn
authors: YW
authors: Liu
authors: Sheng-An
authors: SA
authors: Lee
authors: Chaur-Chin
authors: CC
authors: Chen
authors: Theresa T H
authors: TT
authors: Tsao
authors: Cheng-Yan
authors: CY
authors: Kao
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D012313:RNA / Q000737:chemistry; D012091:Repetitive Sequences, Nucleic Acid; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA