This directory contains the scripts and some raw data used to generate the results.
pipeline/ Folder contains the scripts used to take raw Illumina reads, align, run GATK and snpEFF to detect variants. Scripts used to generate Assembly, Annotation and Orthofinder analysis.
MAT_LOCI/ Has the folder containing all the MAT analysis done to generate both Figure 2 and Supplemental Figure 3.
Rscripts/ Contains all Rscripts (in R Markdown format) used to generate figures depicted in this publication.
Strain_tree/ Contains generated tree files.
OrthoFinder/ contains results generated from OrthoFinder
snpEff/ contains files generated from snpEff analysis.
telomeric-identifier/ contains analysis done for telomere recovery.
coverage/ contains files used in our mosdepth analysis.
