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

<p>To replicate this study the scripts should be ran in&nbsp;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.&nbsp;</p> <p>Step 1: Run dataset_creation_filtering_and_stat_filtering.py</p> <p>Step 2: Run heatmaps_meoids_newick_pcoa.R (Produces Figure 1 and Figure 3b)</p> <p>Step 3: Run dataset_analysis.py</p> <p>Step 4:&nbsp;Run SRA_heatmap_plots.py (Produces Figure 2c)</p> <p>Step 5: Run&nbsp;Figure_3a.R (Produces Figure 3a)</p> <p>Step 6: Run pangenome_plot_MS.py (Produces Figure 3c)</p> <p>&nbsp;</p> <p>&nbsp;</p>