ArticleNAR genomics and bioinformatics2024
ViralFlow v1.0-a computational workflow for streamlining viral genomic surveillance.
Article in NAR genomics and bioinformatics, 2024. 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.
- CAPHEINE, or Everything and the Kitchen Sink: A Workflow for Automating Selection Analyses Using HyPhy.Genome biology and evolution · 2026Article
- Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus.PLoS computational biology · 2026Article
- CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy.bioRxiv : the preprint server for biology · 2026Article
- Oropouche virus outbreaks in northeast Brazil between 2024-25 are characterized by sustained transmission and spread to newly affected areas.PLoS neglected tropical diseases · 2026Article
- Protein language models enable accurate viral host range prediction.Scientific reports · 2026Article
- A bench-to-data analysis workflow for respiratory syncytial virus whole-genome sequencing with short and long-read approaches.Genome medicine · 2026Article
- Revisiting the emergence of the Chikungunya virus in Alagoas, Northeast of Brazil.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Clinical Manifestations and Cytokine Profiles of the Th1, Th2, and Th17 Response Associated with SARS-CoV-2 Omicron Subvariants.Biomedicines · 2025Article
- Oropouche Virus Importation in Southern Brazil and Emerging Concern Calling for Enhanced Public Health Surveillance.Journal of medical virology · 2025Article
- Emergence of Oropouche Virus in Espírito Santo State, Brazil, 2024.Emerging infectious diseases · 2025Article
- Article
- Enhancing SARS-CoV-2 Lineage Surveillance through the Integration of a Simple and Direct qPCR-Based Protocol Adaptation with Established Machine Learning Algorithms.Analytical chemistry · 2024Article
- An Epidemiological Assessment of SARS-CoV-2 in the Sewage System of a Higher Education Institution.Annals of global health · 2024Article
- Multiple introductions and sustained local transmission ofPathogens and global healthArticle
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ViralFlow v1.0 is a computational workflow developed for viral genomic surveillance. Several key changes turned ViralFlow into a general-purpose reference-based genome assembler for all viruses with an available reference genome. New virus-agnostic modules were implemented to further study nucleotide and amino acid mutations. ViralFlow v1.0 runs on a broad range of computational infrastructures, from laptop computers to high-performance computing (HPC) environments, and generates standard and well-formatted outputs suited for both public health reporting and scientific problem-solving. ViralFlow v1.0 is available at: https://viralflow.github.io/index-en.html.
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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.