中央研究院 資訊科學研究所

De novo assembly of RNA-Seq data is essential for transcriptome analysis of organisms without reference genomes. However, it is very challenging to achieve high accuracy in de novo assembly due to the complications arise from sequencing errors, repetitive sequences and chimeric sequences. Here, we introduce a new de novo assembly algorithm, designated EBARDenovo, which stands for Extension, Bridging And Repeat-sensing Denovo for efficient and accurate discovery of transcripts. The algorithm overcomes the problems of sequence repeats and errors by applying the principle of pair-alignment. Moreover, it employs an efficient chimera-detection function to abrogate the effect of aberrant chimeric reads in a sequencing data set.