ArticleScientific reports2022
The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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.
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Who cites it
11 citing papers in PubMed, 21 citations in OpenAlex.
- Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus.PLoS computational biology · 2026Article
- Optimized library preparation, sequencing, and data analysis protocols for the generation of orbivirus consensus sequences.BMC genomics · 2026Article
- MultiVirusConsensus: an accurate and efficient open-source pipeline for identification and consensus sequence generation of multiple viruses from mixed samples.Bioinformatics advances · 2026Article
- Panalyze: automated virus pangenome variation graph construction, analysis and annotation.Bioinformatics advances · 2026Article
- Identification, functional analysis, and clinical applications of defective viral genomes.Frontiers in microbiology · 2025Review
- ViralFlow v1.0-a computational workflow for streamlining viral genomic surveillance.NAR genomics and bioinformatics · 2024Article
- ViralWasm: a client-side user-friendly web application suite for viral genomics.Bioinformatics (Oxford, England) · 2024Article
- A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.PloS one · 2024Article
- COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2.Briefings in bioinformatics · 2023Article
- A hepatitis B virus (HBV) sequence variation graph improves sequence alignment and sample-specific consensus sequence construction for genetic analysis of HBV.bioRxiv : the preprint server for biology · 2023Article
- Rapid genotyping of targeted viral samples using Illumina short-read sequencing data.PloS one · 2022Article
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
Throughout the COVID-19 pandemic, massive sequencing and data sharing efforts enabled the real-time surveillance of novel SARS-CoV-2 strains throughout the world, the results of which provided public health officials with actionable information to prevent the spread of the virus. However, with great sequencing comes great computation, and while cloud computing platforms bring high-performance computing directly into the hands of all who seek it, optimal design and configuration of a cloud compute cluster requires significant system administration expertise. We developed ViReflow, a user-friendly viral consensus sequence reconstruction pipeline enabling rapid analysis of viral sequence datasets leveraging Amazon Web Services (AWS) cloud compute resources and the Reflow system. ViReflow was developed specifically in response to the COVID-19 pandemic, but it is general to any viral pathogen. Importantly, when utilized with sufficient compute resources, ViReflow can trim, map, call variants, and call consensus sequences from amplicon sequence data from 1000 SARS-CoV-2 samples at 1000X depth in < 10 min, with no user intervention. ViReflow's simplicity, flexibility, and scalability make it an ideal tool for viral molecular epidemiological efforts.
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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.