AUTHOR=Yamashita Akifumi , Sekizuka Tsuyoshi , Kuroda Makoto 

TITLE=VirusTAP: Viral Genome-Targeted Assembly Pipeline

JOURNAL=Frontiers in Microbiology

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2016.00032

DOI=10.3389/fmicb.2016.00032

ISSN=1664-302X

ABSTRACT=<p>Although next-generation sequencing (NGS) technology provides a comprehensive means with which to identify potential pathogens from clinical specimens, simple and user-friendly bioinformatics pipelines are expected to obtain the entire viral genome sequence, subsequently providing traceability, based on extensive molecular phylogenetic analyses. We have developed a web-based integrated NGS analysis tool for the viral genome (virus genome-targeted assembly pipeline: VirusTAP), which includes extensive sequence subtraction of host- or bacteria-related NGS reads prior to <italic>de novo</italic> assembly, leading to the prompt and accurate assembly of viral genome sequences from metagenomic NGS reads. The VirusTAP web site is at <ext-link ext-link-type="uri" xlink:href="https://gph.niid.go.jp/cgi-bin/virustap/index.cgi/" xmlns:xlink="http://www.w3.org/1999/xlink">https://gph.niid.go.jp/cgi-bin/virustap/index.cgi/</ext-link>.</p>