MixviR is a tool to help analyze, explore, and visualize high-throughput genomic data from samples that may contain mixed lineages of a given microbial taxon. It was originally developed to analyze SARS-CoV-2 environmental (wastewater) samples, but can be applied to samples from any microbial taxon. It uses vcf-formatted input files along with reference genomic information to identify genetic variants (both at the DNA and amino acid level), and if provided optional input information about lineage-characteristic mutations, can estimate frequencies of target lineages within samples.
MixviR is currently available at https://github.com/mikesovic/MixviR and can be installed with… devtools::install_github(“mikesovic/MixviR/MixviR_X.Y.Z”), after replacing X.Y.Z with the current version.
It has also recently been submitted to CRAN, and once available there, it will be able to be installed with… install.packages(“MixviR”)
Most MixviR analyses will start by running the call_mutations() function, which requires a directory storing one or more vcf files, a fasta-formatted reference genome file, and an annotation file associated with the reference genome that defines genes/open reading frames. If analyzing SARS-CoV-2, a pre-consructed reference object is available (based on the Wuhan reference) and can be specified with reference = “Wuhan”, meaning the sample vcf(s) are the only required input.
The call_mutations() function produces a data frame that can be saved as an object and/or written to a file, and that is used as input for the explore_mutations() and estimate_lineages() functions.
Aside from the vignette associated with the program, we encourage you to use the MixviR Google Group to get help with the program.