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Bioinformatics. 2013 Apr 15;29(8):1004-10. doi: 10.1093/bioinformatics/btt092. Epub 2013 Mar 1.

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

Author information

1
Department of Biomedical informatics, Department of Computer Science and Information Engineering, Asia University, Taichung, Taiwan. htchu@asia.edu.tw

Abstract

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.

PMID:
23457040
DOI:
10.1093/bioinformatics/btt092
[Indexed for MEDLINE]

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