ArticleMicrobiology spectrum2022
VPipe: an Automated Bioinformatics Platform for Assembly and Management of Viral Next-Generation Sequencing Data.
Article in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 15 citations in OpenAlex.
- Complete genome sequences of eight poliovirus Sabin 2-derived and five novel oral poliovirus 2-derived circulating vaccine-derived poliovirus (CVDPV) genomes with single-end recombination from Botswana, 2022-2023.Microbiology resource announcements · 2026Article
- Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.bioRxiv : the preprint server for biology · 2026Article
- Illumina MiSeq and iSeq platforms yield comparable results for viral genomic sequencing.Journal of virological methods · 2025Article
- Unveiling the Future of Infective Endocarditis Diagnosis: The Transformative Role of Metagenomic Next-Generation Sequencing in Culture-Negative Cases.Journal of epidemiology and global health · 2025Review
- Addressing data management and analysis challenges in viral genomics: The Swiss HIV cohort study viral next generation sequencing database.PLOS digital health · 2025Article
- Complete genome sequences of nine double recombinant vaccine-derived novel oral poliovirus type 2 genomes from Nigeria 2023-2024.Microbiology resource announcements · 2024Article
- Complete genome sequences of six S19 poliovirus reference strains.Microbiology resource announcements · 2024Article
- Molecular epidemiology of enteroviruses from Guatemalan wastewater isolated from human lung fibroblasts.PloS one · 2024Article
- Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains.Scientific reports · 2023Article
- Enhanced Viral Metagenomics with Lazypipe 2.Viruses · 2023Article
- Nearly Complete Genome Sequences of Type 2 Sabin-Like Polioviruses from Northern Nigerian Poliovirus Surveillance, 2016 to 2018.Microbiology resource announcements · 2023Article
- Cluster of Norovirus Genogroup IX Outbreaks in Long-Term Care Facilities, Utah, USA, 2021.Emerging infectious diseases · 2022Article
- Genome Sequences of 16 Enterovirus Isolates from Environmental Sewage in Guatemala, 2019 to 2021.Microbiology resource announcements · 2022Article
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Corrections and comments
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Authors and funding
15 authors at 4 institutions in 1 country.
Funding
Abstract
Next-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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.