# vivaldi
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*vivaldi* (**Vi**ral **Va**riant **L**ocation **a**nd **D**iversity) is an R package for analyzing viral genomes using next generation DNA sequencing.

The standard input is a vcf file.

## Installation from CRAN

``` r
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.

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

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

Email: <dg107@nyu.edu>

------------------------------------------------------------------------

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
