ViReMaShiny: an interactive application for analysis of viral recombination data

Jason Yeung, Andrew L. Routh

Research output: Contribution to journalArticlepeer-review

Abstract

MOTIVATION: Recombination is an essential driver of virus evolution and adaption, giving rise to new chimeric viruses, structural variants, sub-genomic RNAs and defective RNAs. Next-generation sequencing (NGS) of virus samples, either from experimental or clinical settings, has revealed a complex distribution of recombination events that contributes to intrahost diversity. We and others have previously developed alignment tools to discover and map these diverse recombination events in NGS data. However, there is no standard for data visualization to contextualize events of interest, and downstream analysis often requires bespoke coding. RESULTS: We present ViReMaShiny, a web-based application built using the R Shiny framework to allow interactive exploration and point-and-click visualization of viral recombination data provided in BED format generated by computational pipelines such as ViReMa (Viral-Recombination-Mapper). AVAILABILITY AND IMPLEMENTATION: The application is hosted at https://routhlab.shinyapps.io/ViReMaShiny/ with associated documentation at https://jayeung12.github.io/. Code is available at https://github.com/routhlab/ViReMaShiny. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)4420-4422
Number of pages3
JournalBioinformatics (Oxford, England)
Volume38
Issue number18
DOIs
StatePublished - Sep 15 2022

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Fingerprint

Dive into the research topics of 'ViReMaShiny: an interactive application for analysis of viral recombination data'. Together they form a unique fingerprint.

Cite this