vAMPirus : A versatile amplicon processing and analysis program for studying viruses

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 a...

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Bibliographic Details
Published in:Molecular ecology resources Vol. 24; no. 6; p. e13978
Main Authors: Veglia, Alex J., Rivera‐Vicéns, Ramón E., Grupstra, Carsten G. B., Howe‐Kerr, Lauren I., Correa, Adrienne M. S.
Format: Journal Article
Language:English
Published: England Wiley Subscription Services, Inc 01.08.2024
Subjects:
Amino acid sequence
Amino acids
Bats
case studies
Coral reefs
corals
data collection
Deoxyribonucleic acid
DNA
DNA sequencing
DNA viruses
dsDNA viruses
Gene sequencing
Nucleotide sequence
Nucleotides
phylogeny
Population dynamics
Population studies
Reproducibility
Ribonucleic acid
RNA
RNA viruses
Sequence analysis
Signal classification
Viruses
Workflow
diversity
RNA
amino acid
DNA
bioinformatics
amplicon sequencing
virus
ISSN:1755-098X, 1755-0998, 1755-0998
Online Access:Get full text
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Summary: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.
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ISSN:1755-098X
1755-0998
1755-0998
DOI:10.1111/1755-0998.13978