V-GAP: Viral genome assembly pipeline

Yoji Nakamura, Motoshige Yasuike, Issei Nishiki, Yuki Iwasaki, Atushi Fujiwara, Yasuhiko Kawato, Toshihiro Nakai, Satoshi Nagai, Takanori Kobayashi, Takashi Gojobori, Mitsuru Ototake

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

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.
Original languageEnglish (US)
Pages (from-to)676-680
Number of pages5
JournalGene
Volume576
Issue number2
DOIs
StatePublished - Oct 25 2015

ASJC Scopus subject areas

  • Genetics

Fingerprint

Dive into the research topics of 'V-GAP: Viral genome assembly pipeline'. Together they form a unique fingerprint.

Cite this