A Combined Approach for <i>de novo</i> DNA Sequence Assembly of Very Short Reads

• Item type: Trans(1)
• 公開日: 2011-11-04
• タイトル: A Combined Approach for <i>de novo</i> DNA Sequence Assembly of Very Short Reads
• タイトル / 言語: en
• タイトル: A Combined Approach for <i>de novo</i> DNA Sequence Assembly of Very Short Reads
• 言語: eng
• キーワード / 主題Scheme: Other
• キーワード / 主題: Original Paper
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_6501
• 資源タイプ: journal article
• 著者所属: Graduate School of Information and Engineering, Tokyo Institute of Technology
• 著者所属: Graduate School of Information and Engineering, Tokyo Institute of Technology
• 著者所属: Graduate School of Information and Engineering, Tokyo Institute of Technology
• 著者所属(英): en
• 著者所属(英): Graduate School of Information and Engineering, Tokyo Institute of Technology
• 著者所属(英): en
• 著者所属(英): Graduate School of Information and Engineering, Tokyo Institute of Technology
• 著者所属(英): en
• 著者所属(英): Graduate School of Information and Engineering, Tokyo Institute of Technology
• 著者名: WisnuAnantaKusuma; Takashi, Ishida; Yutaka, Akiyama
• 著者名(英): Wisnu, AnantaKusuma; Takashi, Ishida; Yutaka, Akiyama
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: De novo DNA sequence assembly is very important in genome sequence analysis. In this paper, we investigated two of the major approaches for De novo DNA sequence assembly of very short reads: overlap-layout-consensus (OLC) and Eulerian path. From that investigation, we developed a new assembly technique by combining the OLC and the Eulerian path methods in a hierarchical process. The contigs yielded by these two approaches were treated as reads and were assembled again to yield longer contigs. We tested our approach using three real very-short-read datasets generated by an Illumina Genome Analyzer and four simulated very-short-read datasets that contained sequencing errors. The sequencing errors were modeled based on Illumina's sequencing technology. As a result, our combined approach yielded longer contigs than those of Edena (OLC) and Velvet (Eulerian path) in various coverage depths and was comparable to SOAPdenovo, in terms of N50 size and maximum contig lengths. The assembly results were also validated by comparing contigs that were produced by assemblers with their reference sequence from an NCBI database. The results show that our approach produces more accurate results than Velvet, Edena, and SOAPdenovo alone. This comparison indicates that our approach is a viable way to assemble very short reads from next generation sequencers.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: De novo DNA sequence assembly is very important in genome sequence analysis. In this paper, we investigated two of the major approaches for De novo DNA sequence assembly of very short reads: overlap-layout-consensus (OLC) and Eulerian path. From that investigation, we developed a new assembly technique by combining the OLC and the Eulerian path methods in a hierarchical process. The contigs yielded by these two approaches were treated as reads and were assembled again to yield longer contigs. We tested our approach using three real very-short-read datasets generated by an Illumina Genome Analyzer and four simulated very-short-read datasets that contained sequencing errors. The sequencing errors were modeled based on Illumina's sequencing technology. As a result, our combined approach yielded longer contigs than those of Edena (OLC) and Velvet (Eulerian path) in various coverage depths and was comparable to SOAPdenovo, in terms of N50 size and maximum contig lengths. The assembly results were also validated by comparing contigs that were produced by assemblers with their reference sequence from an NCBI database. The results show that our approach produces more accurate results than Velvet, Edena, and SOAPdenovo alone. This comparison indicates that our approach is a viable way to assemble very short reads from next generation sequencers.
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AA12177013
• 書誌情報: IPSJ Transactions on Bioinformatics（TBIO）; 巻 4, p. 21-33, 発行日 2011-11-04
• ISSN / 収録物識別子タイプ: ISSN
• ISSN / 収録物識別子: 1882-6679
• 出版者 / 言語: ja
• 出版者: 情報処理学会