Viral Variant Location and Diversity

Analysis of minor alleles in Illumina sequencing data of viral genomes. Functions in 'vivaldi' primarily operate on vcf files.

vivaldi

vivaldi (Viral Variant Location and Diversity) is an R package for analyzing viral genomes using next generation DNA sequencing.

The standard input is a vcf file.

Installation from CRAN

install.packages("vivaldi")

Install development version from github

To get a bug fix or to use a feature from the development version, you can install the development version of vivaldi from GitHub.

# install.packages("devtools")
devtools::install_github("GreshamLab/vivaldi")

Authors: Marrisa Knoll, Katherine Johnson, Megan Hockman, Eric Borenstein, Mohammed Khalfan, Elodie Ghedin, David Gresham

Email: [email protected]

If you use vivaldi in published research, please cite:

Roder, A. E., et al. "Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data." bioRxiv (2022): 2021-05 URL https://www.biorxiv.org/content/10.1101/2021.05.05.442873v2