{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T19:02:20Z","timestamp":1762542140360},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0cykao@csie.ntu.edu.tw, htchu@asia.edu.tw or postergrey@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt092","type":"journal-article","created":{"date-parts":[[2013,3,2]],"date-time":"2013-03-02T10:23:13Z","timestamp":1362219793000},"page":"1004-1010","source":"Crossref","is-referenced-by-count":28,"title":["EBARDenovo: highly accurate <i>de novo<\/i> assembly of RNA-Seq with efficient chimera-detection"],"prefix":"10.1093","volume":"29","author":[{"given":"Hsueh-Ting","family":"Chu","sequence":"first","affiliation":[{"name":"1 Department of Biomedical informatics, 2Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan, 3BCCDC Public Health Microbiology & Reference Laboratory, Vancouver, British Columbia V5Z 4R4, Canada, 4Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 4R4, Canada, 5Institute of Biotechnology, 6Graduate Institute of Biomedical Electronics and Bioinformatics, 7Department of Computer Science and Information Engineering, National Taiwan University, Taipei 10617, Taiwan, 8National Research Institute of Chinese Medicine, No. 155-1, Sec. 2, Li Nung Street Peitou, Taipei 11221, Taiwan, 9Department of Information Management, Kainan University, Taoyuan, 33857, Taiwan and 10Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan"},{"name":"1 Department of Biomedical informatics, 2Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan, 3BCCDC Public Health Microbiology & Reference Laboratory, Vancouver, British Columbia V5Z 4R4, Canada, 4Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 4R4, Canada, 5Institute of Biotechnology, 6Graduate Institute of Biomedical Electronics and Bioinformatics, 7Department of Computer Science and Information Engineering, National Taiwan University, Taipei 10617, Taiwan, 8National Research Institute of Chinese Medicine, No. 155-1, Sec. 2, Li Nung Street Peitou, Taipei 11221, Taiwan, 9Department of Information Management, Kainan University, Taoyuan, 33857, Taiwan and 10Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William W. L.","family":"Hsiao","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical informatics, 2Department of Computer Science and Information Engineering, Asia University, Taichung 41354, Taiwan, 3BCCDC Public Health Microbiology & Reference Laboratory, Vancouver, British Columbia V5Z 4R4, Canada, 4Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V5Z 4R4, Canada, 5Institute of Biotechnology, 6Graduate Institute of Biomedical Electronics and Bioinformatics, 7Department of Computer Science and Information Engineering, National Taiwan University, Taipei 10617, Taiwan, 8National Research Institute of Chinese Medicine, No. 155-1, Sec. 2, Li Nung Street Peitou, Taipei 11221, Taiwan, 9Department of Information Management, Kainan University, Taoyuan, 33857, Taiwan and 10Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan"},{"name":"1 Department of Biomedical informatics, 2Department of 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