VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.

Content Provider	Europe PMC
Author	Wagner, Darlene D. Marine, Rachel L. Ramos, Edward Ng, Terry Fei Fan Castro, Christina J. Okomo-Adhiambo, Margaret Harvey, Krysten Doho, Gregory Kelly, Reagan Jain, Yatish Tatusov, Roman L. Silva, Hideky Rota, Paul A. Khan, Agha N. Oberste, M. Steven
Editor	Chen, Wei-Hua
Abstract	ABSTRACTNext-generation sequencing (NGS) is a powerful tool for detecting and investigating viral pathogens; however, analysis and management of the enormous amounts of data generated from these technologies remains a challenge. Here, we present VPipe (the Viral NGS Analysis Pipeline and Data Management System), an automated bioinformatics pipeline optimized for whole-genome assembly of viral sequences and identification of diverse species. VPipe automates the data quality control, assembly, and contig identification steps typically performed when analyzing NGS data. Users access the pipeline through a secure web-based portal, which provides an easy-to-use interface with advanced search capabilities for reviewing results. In addition, VPipe provides a centralized system for storing and analyzing NGS data, eliminating common bottlenecks in bioinformatics analyses for public health laboratories with limited on-site computational infrastructure. The performance of VPipe was validated through the analysis of publicly available NGS data sets for viral pathogens, generating high-quality assemblies for 12 data sets. VPipe also generated assemblies with greater contiguity than similar pipelines for 41 human respiratory syncytial virus isolates and 23 SARS-CoV-2 specimens.IMPORTANCE Computational infrastructure and bioinformatics analysis are bottlenecks in the application of NGS to viral pathogens. As of September 2021, VPipe has been used by the U.S. Centers for Disease Control and Prevention (CDC) and 12 state public health laboratories to characterize >17,500 and 1,500 clinical specimens and isolates, respectively. VPipe automates genome assembly for a wide range of viruses, including high-consequence pathogens such as SARS-CoV-2. Such automated functionality expedites public health responses to viral outbreaks and pathogen surveillance.
Page Count	10
Volume Number	10
PubMed Central reference number	PMC8941893
Issue Number	2
PubMed reference number	35234489
Journal	Microbiology Spectrum [Microbiol Spectr]
e-ISSN	21650497
DOI	10.1128/spectrum.02564-21
Language	English
Publisher	American Society for Microbiology
Publisher Date	2022-03-02
Publisher Place	N.W., Washington, DC
Access Restriction	Open
Rights License	This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.
Subject Keyword	next-generation sequencing (NGS) automated bioinformatics pipeline viral molecular detection infectious disease surveillance
Content Type	Text
Resource Type	Article
Subject	Cell Biology Physiology Infectious Diseases Immunology and Microbiology Genetics Microbiology (medical) Ecology