Pairwise SNP differences

This is an R script to obtain summaries of pairwise SNP differences for any grouping of samples (e.g., MLST groups, monophyletic clades, etc).

Downloading the script

Clone the git-hub repository. Information on the bar to the right of this window.

How it works

The script can be run from the command line:

Rscript<.exe> summarise_snp_differences.R --help

Or, from within R. Details of variables that should be changed can be found in the script header.

Tutorial

A brief tutorial describing the background can be found in the file:

pairwise_snp_differences.pdf

RStudio

The whole repo can be cloned, and opened as an RStudio project. Within RStudio the .Rmd file can be easily made into an .html file for viewing in a web-browser.