V-GAP: Viral genome assembly pipeline

Handle URI:
http://hdl.handle.net/10754/581472
Title:
V-GAP: Viral genome assembly pipeline
Authors:
Nakamura, Yoji; Yasuike, Motoshige; Nishiki, Issei; Iwasaki, Yuki; Fujiwara, Atushi; Kawato, Yasuhiko; Nakai, Toshihiro; Nagai, Satoshi; Kobayashi, Takanori; Gojobori, Takashi ( 0000-0001-7850-1743 ) ; Ototake, Mitsuru
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.
KAUST Department:
Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
V-GAP: Viral genome assembly pipeline 2015 Gene
Publisher:
Elsevier BV
Journal:
Gene
Issue Date:
22-Oct-2015
DOI:
10.1016/j.gene.2015.10.029
Type:
Article
ISSN:
03781119
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S0378111915012378
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorNakamura, Yojien
dc.contributor.authorYasuike, Motoshigeen
dc.contributor.authorNishiki, Isseien
dc.contributor.authorIwasaki, Yukien
dc.contributor.authorFujiwara, Atushien
dc.contributor.authorKawato, Yasuhikoen
dc.contributor.authorNakai, Toshihiroen
dc.contributor.authorNagai, Satoshien
dc.contributor.authorKobayashi, Takanorien
dc.contributor.authorGojobori, Takashien
dc.contributor.authorOtotake, Mitsuruen
dc.date.accessioned2015-11-01T10:59:46Zen
dc.date.available2015-11-01T10:59:46Zen
dc.date.issued2015-10-22en
dc.identifier.citationV-GAP: Viral genome assembly pipeline 2015 Geneen
dc.identifier.issn03781119en
dc.identifier.doi10.1016/j.gene.2015.10.029en
dc.identifier.urihttp://hdl.handle.net/10754/581472en
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.en
dc.language.isoenen
dc.publisherElsevier BVen
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S0378111915012378en
dc.rightsUnder a Creative Commons license. http://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectNext-generation sequencingen
dc.subjectDe novo assemblyen
dc.subjectShotgun sequencesen
dc.subjectVirus genomesen
dc.titleV-GAP: Viral genome assembly pipelineen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalGeneen
dc.eprint.versionPublisher's Version/PDFen
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, Japanen
dc.contributor.institutionNational Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minami-ise, Mie 516-0193, Japanen
dc.contributor.institutionGraduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japanen
dc.contributor.institutionCenter for Information Biology, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japanen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorGojobori, Takashien
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