title: V-GAP: Viral genome assembly pipeline.
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.
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan. Electronic address: yojnakam@affrc.go.jp.
authors.forename: Yoji
authors.initials: Y
authors.lastname: Nakamura
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan.
authors.forename: Motoshige
authors.initials: M
authors.lastname: Yasuike
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan.
authors.forename: Issei
authors.initials: I
authors.lastname: Nishiki
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Iwasaki
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan. Electronic address: jiwara@affrc.go.jp.
authors.forename: Atushi
authors.initials: A
authors.lastname: Fujiwara
authors.affiliation: National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minami-ise, Mie 516-0193, Japan.
authors.forename: Yasuhiko
authors.initials: Y
authors.lastname: Kawato
authors.affiliation: Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan.
authors.forename: Toshihiro
authors.initials: T
authors.lastname: Nakai
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nagai
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan.
authors.forename: Takanori
authors.initials: T
authors.lastname: Kobayashi
authors.affiliation: Computational Bioscience Research Center, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Center for Information Biology, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.affiliation: Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan.
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Ototake
mesh_terms: D001435:Bacteriophages / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*
chemical_list: D004279:DNA, Viral
keywords: De novo assembly; Next-generation sequencing; Shotgun sequences; Virus genomes