ArticleViruses2022
ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection.
Article in Viruses, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed, 75 citations in OpenAlex.
- Immunogenicity and safety of CoronaVac vaccine in children and adolescents (Immunita-002, Brazil): A phase IV six-month follow up.Scientific reports · 2025Trial
- Immunogenicity, Effectiveness, and Safety of Inactivated Virus (CoronaVac) Vaccine in a Two-Dose Primary Protocol and BNT162b2 Heterologous Booster in Brazil (Immunita-001): A One Year Period Follow Up Phase 4 Study.Frontiers in immunology · 2022Trial
- From Bench to Insight: Rapid Pathogen Genomic Surveillance Workflow for SARS-CoV-2 and Emerging Pathogens.Genes · 2026Article
- An evaluation of computational methods for reconstruction of human viral DNA genomes.GigaScience · 2026Article
- Sustained Oropouche virus transmission in Rio de Janeiro's Atlantic Forest: genomic evidence over a two-year period.Memorias do Instituto Oswaldo Cruz · 2026Article
- Clinical Manifestations and Cytokine Profiles of the Th1, Th2, and Th17 Response Associated with SARS-CoV-2 Omicron Subvariants.Biomedicines · 2025Article
- Entomo-Virological Surveillance and Genomic Insights into DENV-2 Genotype III Circulation in Rural Esmeraldas, Ecuador.Pathogens (Basel, Switzerland) · 2025Article
- Clinical characteristics, SARS-CoV-2 variants, and outcomes of adults hospitalized due to COVID-19 in Latin American countries.Clinics (Sao Paulo, Brazil) · 2025Observational
- Replication differences of SARS-CoV-2 lineages may arise from unique RNA replication characteristics and nucleocapsid protein expression.Frontiers in cellular and infection microbiology · 2025Article
- Higher frequency of interstate over international transmission chains of SARS-CoV-2 virus at the Rio Grande do Sul - Brazil state borders.Virus research · 2025Article
- Molecular Epidemiology of Western Equine Encephalitis Virus, South America, 2023-2024.Emerging infectious diseases · 2024Article
- Long-term surveillance of SARS-CoV-2 in the school community from Campo Grande, Brazil.BMC public health · 2024Article
- Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco-Brazil.Microbiology spectrum · 2024Article
- ViralFlow v1.0-a computational workflow for streamlining viral genomic surveillance.NAR genomics and bioinformatics · 2024Article
- Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023.Microbiology spectrum · 2024Article
- Whole Genome Sequencing of DENV-2 isolated frombioRxiv : the preprint server for biology · 2024Article
- V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.GigaScience · 2024Article
- Cohort profile: follow-up of a household cohort throughout five epidemic waves of SARS-CoV-2 in Rio de Janeiro, Brazil.Cadernos de saude publica · 2024Article
- A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.PloS one · 2024Article
- Long-term co-circulation of multiple arboviruses in southeast Australia revealed by xeno-monitoring and viral whole-genome sequencing.Virus evolution · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
The COVID-19 pandemic is driven by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) that emerged in 2019 and quickly spread worldwide. Genomic surveillance has become the gold standard methodology used to monitor and study this fast-spreading virus and its constantly emerging lineages. The current deluge of SARS-CoV-2 genomic data generated worldwide has put additional pressure on the urgent need for streamlined bioinformatics workflows. Here, we describe a workflow developed by our group to process and analyze large-scale SARS-CoV-2 Illumina amplicon sequencing data. This workflow automates all steps of SARS-CoV-2 reference-based genomic analysis: data processing, genome assembly, PANGO lineage assignment, mutation analysis and the screening of intrahost variants. The pipeline is capable of processing a batch of around 100 samples in less than half an hour on a personal laptop or in less than five minutes on a server with 50 threads. The workflow presented here is available through Docker or Singularity images, allowing for implementation on laptops for small-scale analyses or on high processing capacity servers or clusters. Moreover, the low requirements for memory and CPU cores and the standardized results provided by ViralFlow highlight it as a versatile tool for SARS-CoV-2 genomic analysis.
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What OpenQuestion holds
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.