Knowledge Resource Center for Ecological Environment in Arid Area
| DOI | 10.1093/bioinformatics/btt092 |
| EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection | |
| Chu, Hsueh-Ting1,2; Hsiao, William W. L.3,4; Chen, Jen-Chih5; Yeh, Tze-Jung5; Tsai, Mong-Hsun5,6; Lin, Han7; Liu, Yen-Wenn8; Lee, Sheng-An9; Chen, Chaur-Chin10; Tsao, Theresa T. H.6,7; Kao, Cheng-Yan6,7 | |
| 通讯作者 | Tsao, Theresa T. H. |
| 来源期刊 | BIOINFORMATICS
 |
| ISSN | 1367-4803 |
| EISSN | 1460-2059 |
| 出版年 | 2013 |
| 卷号 | 29期号:8页码:1004-1010 |
| 英文摘要 | 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. Supplementary information: Supplementary data are available at Bioinformatics online. |
| 类型 | Article |
| 语种 | 英语 |
| 国家 | Taiwan ; Canada |
| 收录类别 | SCI-E |
| WOS记录号 | WOS:000318109300006 |
| WOS关键词 | TRANSCRIPTOME ; EXPRESSION ; SEQUENCES ; ALIGNMENT ; EST |
| WOS类目 | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| 资源类型 | 期刊论文 |
| 条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/176143 |
| 作者单位 | 1.Asia Univ, Dept Biomed informat, Taichung 41354, Taiwan; 2.Asia Univ, Dept Comp Sci & Informat Engn, Taichung 41354, Taiwan; 3.BCCDC Publ Hlth Microbiol & Reference Lab, Vancouver, BC V5Z 4R4, Canada; 4.Univ British Columbia, Dept Pathol & Lab Med, Vancouver, BC V5Z 4R4, Canada; 5.Natl Taiwan Univ, Inst Biotechnol, Taipei 10617, Taiwan; 6.Natl Taiwan Univ, Grad Inst Biomed Elect & Bioinformat, Taipei 10617, Taiwan; 7.Natl Taiwan Univ, Dept Comp Sci & Informat Engn, Taipei 10617, Taiwan; 8.Natl Res Inst Chinese Med, Taipei 11221, Taiwan; 9.Kainan Univ, Dept Informat Management, Tao Yuan 33857, Taiwan; 10.Natl Tsing Hua Univ, Dept Comp Sci, Hsinchu 30013, Taiwan |
| 推荐引用方式 GB/T 7714 | Chu, Hsueh-Ting,Hsiao, William W. L.,Chen, Jen-Chih,et al. EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection[J],2013,29(8):1004-1010. |
| APA | Chu, Hsueh-Ting.,Hsiao, William W. L..,Chen, Jen-Chih.,Yeh, Tze-Jung.,Tsai, Mong-Hsun.,...&Kao, Cheng-Yan.(2013).EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.BIOINFORMATICS,29(8),1004-1010. |
| MLA | Chu, Hsueh-Ting,et al."EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection".BIOINFORMATICS 29.8(2013):1004-1010. |
| 条目包含的文件 | 条目无相关文件。 | |||||
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