ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance-Reference-Cited by-同舟云学术

ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance

Published:2024-04-04 Issue:2 Volume:6 Page:
ISSN:2631-9268
Container-title:NAR Genomics and Bioinformatics
language:en
Short-container-title:

Author:

da Silva Alexandre Freitas¹²,da Silva Neto Antonio Marinho³,Aksenen Cleber Furtado⁴,Jeronimo Pedro Miguel Carneiro⁴,Dezordi Filipe Zimmer¹²,Almeida Suzana Porto⁴,Costa Hudson Marques Paula²,Salvato Richard Steiner⁵,Campos Tulio de Lima²,Wallau Gabriel da Luz¹²⁶^ORCID,of the Fiocruz Genomic Network on behalf

Affiliation:

1. Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ , Recife , Pernambuco 50670-420 , Brazil

2. Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ , Recife , Pernambuco 50670-420 , Brazil

3. Data Analysis and Engineering, Genomic Surveillance Unit, Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton , Cambridgeshire CB10 1SA , UK

4. Fundação Oswaldo Cruz (Fiocruz) - Fiocruz-CE, Eusebio , Ceará 61760-000 , Brazil

5. Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública , Porto Alegre , Rio Grande do Sul 90450-190 , Brazil

6. Department of Arbovirology, Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Center for Arbovirus and Hemorrhagic Fever Reference and Research, National Reference Center for Tropical Infectious Diseases , Bernhard-Nocht-Strasse 74 , D-20359 Hamburg , Germany

Abstract

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.

Funder

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior

Centers for Disease Control and Prevention

Brazilian Ministry of Health

Vice Presidency of Research and Biological Collections

Fiocruz Technological Platforms

Conselho Nacional de Desenvolvimento Científico e Tecnológico

Publisher

Oxford University Press (OUP)

Link

https://academic.oup.com/nargab/article-pdf/6/2/lqae056/57907529/lqae056.pdf

Reference30 articles.