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dc.contributor.authorNakamura, Yoji
dc.contributor.authorYasuike, Motoshige
dc.contributor.authorNishiki, Issei
dc.contributor.authorIwasaki, Yuki
dc.contributor.authorFujiwara, Atushi
dc.contributor.authorKawato, Yasuhiko
dc.contributor.authorNakai, Toshihiro
dc.contributor.authorNagai, Satoshi
dc.contributor.authorKobayashi, Takanori
dc.contributor.authorGojobori, Takashi
dc.contributor.authorOtotake, Mitsuru
dc.date.accessioned2015-11-01T10:59:46Z
dc.date.available2015-11-01T10:59:46Z
dc.date.issued2015-10-22
dc.identifier.citationV-GAP: Viral genome assembly pipeline 2015 Gene
dc.identifier.issn03781119
dc.identifier.pmid26475935
dc.identifier.doi10.1016/j.gene.2015.10.029
dc.identifier.urihttp://hdl.handle.net/10754/581472
dc.description.abstractNext-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.
dc.language.isoen
dc.publisherElsevier BV
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S0378111915012378
dc.rightsUnder a Creative Commons license. http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectNext-generation sequencing
dc.subjectDe novo assembly
dc.subjectShotgun sequences
dc.subjectVirus genomes
dc.titleV-GAP: Viral genome assembly pipeline
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.identifier.journalGene
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionResearch Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan
dc.contributor.institutionNational Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minami-ise, Mie 516-0193, Japan
dc.contributor.institutionGraduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
dc.contributor.institutionCenter for Information Biology, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personGojobori, Takashi
refterms.dateFOA2018-06-13T11:08:32Z


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