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Updated: May 13, 2026

Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection
Hsueh-Ting Chu1, William W L Hsiao, Jen-Chih Chen
1Department of Biomedical informatics, Department of Computer Science and Information Engineering, Asia University, Taichung, Taiwan. htchu@asia.edu.tw
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 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.
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.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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