Mash-based analyses of E. coli genomes reveal 14 distinct phylogroups

To replicate this study the scripts should be ran in the following order. It is expected that you download and unzip the Data.zip file and replace the variable `input_root_folder` in all scripts with the complete file path of the folder where the unzipped Data folder is. Step 1: Run dataset_creation_filtering_and_stat_filtering.py Step 2: Run heatmaps_meoids_newick_pcoa.R (Produces Figure 1 and Figure 3b) Step 3: Run dataset_analysis.py Step 4: Run SRA_heatmap_plots.py (Produces Figure 2c) Step 5: Run Figure_3a.R (Produces Figure 3a) Step 6: Run pangenome_plot_MS.py (Produces Figure 3c)