VirusTAP: Viral Genome-Targeted Assembly Pipeline
نویسندگان
چکیده
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/.
منابع مشابه
VirAmp: a galaxy-based viral genome assembly pipeline
BACKGROUND Advances in next generation sequencing make it possible to obtain high-coverage sequence data for large numbers of viral strains in a short time. However, since most bioinformatics tools are developed for command line use, the selection and accessibility of computational tools for genome assembly and variation analysis limits the ability of individual labs to perform further bioinfor...
متن کاملNew Anti-Influenza Agents: Targeting the Virus Entry and Genome Transcription
Introduction: The emergence and spread of the pandemic H1N1 influenza virus in 2009 indicates a limitation in the strategy to control the infection, despite a long-established vaccination programme and approved antivirals. Production the proper vaccine against influenza is difficult due to the genetic recombination of virus in the event of pandemic and co-circulation of drug-resistance variants...
متن کاملKollector: transcript-informed, targeted de novo assembly of gene loci
Motivation Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise. A targeted assembly approach to perform local assembly of sequences of interest remains a valuable option for some applications. This is especially true for ...
متن کاملdrVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes
Background Virus discovery using high-throughput next-generation sequencing has become more commonplace. However, although analysis of deep next-generation sequencing data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple an...
متن کاملBenchmarking viromics: an in silico evaluation of metagenome-enabled estimates of viral community composition and diversity
BACKGROUND Viral metagenomics (viromics) is increasingly used to obtain uncultivated viral genomes, evaluate community diversity, and assess ecological hypotheses. While viromic experimental methods are relatively mature and widely accepted by the research community, robust bioinformatics standards remain to be established. Here we used in silico mock viral communities to evaluate the viromic s...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Frontiers in microbiology
دوره 7 شماره
صفحات -
تاریخ انتشار 2016