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vAMPirus: A versatile amplicon processing and analysis program for studying viruses
  • +2
  • Alex Veglia,
  • Ramon E Rivera-Vicens,
  • Carsten Grupstra,
  • Lauren Howe-Kerr,
  • Adrienne Correa
Alex Veglia
Rice University

Corresponding Author:alex.veglia@gmail.com

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Ramon E Rivera-Vicens
Inter American University of Puerto Rico - Barranquitas Campus
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Carsten Grupstra
Boston University
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Lauren Howe-Kerr
Rice University
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Adrienne Correa
Rice University
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Abstract

Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user-friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide- and amino acid-based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies, and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal-to-noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double-stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef-associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization, and communication of virus lineage-specific analyses. The vAMPirus framework is designed to be adaptable; community-driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.
05 Apr 2024Submitted to Molecular Ecology Resources
08 Apr 2024Submission Checks Completed
08 Apr 2024Assigned to Editor
08 Apr 2024Review(s) Completed, Editorial Evaluation Pending
10 Apr 2024Reviewer(s) Assigned
08 May 2024Editorial Decision: Accept