EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection
| Autor: | Sheng-An Lee, William W. L. Hsiao, Chaur-Chin Chen, Theresa Tsun-Hui Tsao, Mong-Hsun Tsai, Jen-Chih Chen, Han Lin, Hsueh-Ting Chu, Tze-Jung Yeh, Cheng-Yan Kao, Yen-Wenn Liu |
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| Rok vydání: | 2013 |
| Předmět: |
Statistics and Probability
Sequence Analysis RNA Computer science Gene Expression Profiling Repetitive Sequences Sequence assembly RNA-Seq Computational biology Amplicon Biochemistry De Bruijn graph Computer Science Applications Computational Mathematics Chimera (genetics) symbols.namesake Computational Theory and Mathematics symbols RNA natural sciences Molecular Biology Algorithm Algorithms Software Repetitive Sequences Nucleic Acid |
| Zdroj: | Bioinformatics. 29:1004-1010 |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/btt092 |
| Popis: | 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. Contact: cykao@csie.ntu.edu.tw, htchu@asia.edu.tw or postergrey@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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