Yamashita Akifumi, Sekizuka Tsuyoshi, Kuroda Makoto
Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan.
Front Microbiol. 2016 Feb 2;7:32. doi: 10.3389/fmicb.2016.00032. eCollection 2016.
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 de novo assembly, leading to the prompt and accurate assembly of viral genome sequences from metagenomic NGS reads. The VirusTAP web site is at https://gph.niid.go.jp/cgi-bin/virustap/index.cgi/.
尽管下一代测序（NGS）技术提供了一种从临床标本中鉴定潜在病原体的综合方法，但基于广泛的分子系统发育分析，人们期望简单且用户友好的生物信息学流程能够获得完整的病毒基因组序列，从而实现溯源。我们开发了一种基于网络的病毒基因组NGS综合分析工具（病毒基因组靶向组装流程：VirusTAP），该工具在从头组装之前，对与宿主或细菌相关的NGS读数进行广泛的序列扣除，从而能够从宏基因组NGS读数中快速准确地组装病毒基因组序列。VirusTAP网站为https://gph.niid.go.jp/cgi-bin/virustap/index.cgi/ 。
