High accuracy de novo assembly of the short sequencing reads from RNA-Seq technology is very challenging. A team led by researchers at Asia University, Taiwan have developed a de novo assembly algorithm, EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo. This algorithm employs an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in RNA-Seq data.
EBARDenovo resolves the complications of RNA-Seq assembly arising from sequencing errors, repetitive sequences and aberrant chimeric amplicons. In a series of assembly experiments, this algorithm was found to be the most accurate among the examined programs including de Bruijn graph assemblers, Trinity and Oases.
AVAILABILITY: EBARDenovo is freely available at http://ebardenovo.sourceforge.net/
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Chu HT, Hsiao WW, Chen JC, Yeh TJ, Tsai MH, Lin H, Liu YW, Lee SA, Chen CC, Tsao TT, Kao CY. (2013) EBARDenovo: Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. Bioinformatics [Epub ahead of print]. [abstract]