Motivation: 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

more »

... meric 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. Availability and implementation: EBARDenovo is available at http:// ebardenovo.sourceforge.net/. This software package (with patent pending) is free of charge for academic use only.