文章基本信息

标题：Double Assembly Method with Characteristics of k-mer's Coverage for Contig
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作者：Ayako OHSHIRO ; Takeo OKAZAKI ; Morikazu NAKAMURA 等
期刊名称：International Journal of Computer Science and Network Security
印刷版ISSN：1738-7906
出版年度：2014
卷号：14
期号：2
页码：54-61
出版社：International Journal of Computer Science and Network Security
摘要：Reads sequences from giga sequencer with parallel processing include many read errors. Various de Novo assembly methods by use of k-mer has been proposed in order to remove read error region and derive contigs, such as Velvet, ABySS, SSAKE and so on. Hybrid assembly algorithms by integrating the results of traditional assembly method have been proposed such as MAIA and GAA. Because assembly result depends on assembly algorithm and k value, it is difficult to obtain assembly results robustly. In this paper, we designed a double assembly method merging different k-mers and applied it to combining rules with a characteristic distribution of k-mer's coverage value for contig. We compared our proposed method with traditional assembly method to evaluate the effectiveness. The experiment was carried out by use of E. coli data and evaluated its performance with coverage ratio, the correct ratio of output contigs.
关键词：DNA double assembly; k-mer; coverage; characteristic distribution