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    V-GAP: Viral genome assembly pipeline

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    Description:
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    Type
    Article
    Authors
    Nakamura, Yoji
    Yasuike, Motoshige
    Nishiki, Issei
    Iwasaki, Yuki
    Fujiwara, Atushi
    Kawato, Yasuhiko
    Nakai, Toshihiro
    Nagai, Satoshi
    Kobayashi, Takanori
    Gojobori, Takashi cc
    Ototake, Mitsuru
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computational Bioscience Research Center (CBRC)
    Date
    2015-10-25
    Online Publication Date
    2015-10-25
    Print Publication Date
    2016-02
    Permanent link to this record
    http://hdl.handle.net/10754/581472
    
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    Abstract
    Next-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.
    Citation
    V-GAP: Viral genome assembly pipeline 2015 Gene
    Publisher
    Elsevier BV
    Journal
    Gene
    DOI
    10.1016/j.gene.2015.10.029
    PubMed ID
    26475935
    Additional Links
    http://linkinghub.elsevier.com/retrieve/pii/S0378111915012378
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.gene.2015.10.029
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC)

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