EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection

Hsueh-Ting Chu, William W. L. Hsiao, Jen-Chih Chen, Tze-Jung Yeh, Mong-Hsun Tsai, Han Lin, Yen-Wenn Liu, Sheng-An Lee, Chaur-Chin Chen, Theresa T. H. Tsao, Cheng-Yan Kao
2013 Computer applications in the biosciences : CABIOS  
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.
doi:10.1093/bioinformatics/btt092 pmid:23457040 fatcat:6cnu5tvwx5aptc6omwwefyuwhu