vAMPirus: A versatile amplicon processing and analysis program for studying viruses.
| Title: | vAMPirus: A versatile amplicon processing and analysis program for studying viruses. |
|---|---|
| Authors: | Veglia AJ; BioSciences Department, Rice University, Houston, Texas, USA.; Department of Biology, University of Puerto Rico Mayagüez, Mayagüez, Puerto Rico, USA.; EcoAzul, La Parguera, Puerto Rico, USA.; Rivera-Vicéns RE; EcoAzul, La Parguera, Puerto Rico, USA.; Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.; Department of Sciences and Technology, Interamerican University of Puerto Rico at Barranquitas, Barranquitas, Puerto Rico, USA.; Grupstra CGB; BioSciences Department, Rice University, Houston, Texas, USA.; Department of Biology, Boston University, Boston, Massachusetts, USA.; Howe-Kerr LI; BioSciences Department, Rice University, Houston, Texas, USA.; Minderoo Foundation, Perth, Western Australia, Australia.; Correa AMS; BioSciences Department, Rice University, Houston, Texas, USA.; Department of Environmental Science, Policy, and Management, University of California, California, USA. |
| Source: | Molecular ecology resources [Mol Ecol Resour] 2024 Aug; Vol. 24 (6), pp. e13978. Date of Electronic Publication: 2024 May 22. |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Blackwell Country of Publication: England NLM ID: 101465604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1755-0998 (Electronic) Linking ISSN: 1755098X NLM ISO Abbreviation: Mol Ecol Resour Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Oxford, England : Blackwell |
| MeSH Terms: | Software*; Computational Biology/methods ; DNA Viruses/genetics ; DNA Viruses/classification ; Viruses/genetics ; Viruses/classification ; Viruses/isolation & purification ; RNA Viruses/genetics ; RNA Viruses/classification ; RNA Viruses/isolation & purification ; Phylogeny |
| 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.; (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.) |
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| Grant Information: | OCE 22-24354 Directorate for Biological Sciences; OCE-2145472 Directorate for Biological Sciences; Wagoner Foreign Study Award; Kirk W. Dotson Endowed Graduate Fellowship in Ecology and Evolutionary Biology; Lewis and Clark Grants for Exploration; 100009646 Gulf Research Program of the National Academies of Sciences |
| Contributed Indexing: | Keywords: DNA; RNA; amino acid; amplicon sequencing; bioinformatics; diversity; virus |
| Entry Date(s): | Date Created: 20240522 Date Completed: 20240730 Latest Revision: 20240730 |
| Update Code: | 20260130 |
| DOI: | 10.1111/1755-0998.13978 |
| PMID: | 38775206 |
| Database: | MEDLINE |
Journal Article