├── .gitignore ├── README.md ├── Snakefile ├── analyze-flanking-regions.py ├── beta-lactamases ├── README.md ├── Snakefile ├── analysis │ ├── 01_make_breakpoint_plots.sh │ ├── 02_make_CTX-M-65_figure.sh │ ├── 03_make_breakpoint_AUC_plots.R │ ├── 04_make_entropy_transposase_curves.sh │ ├── 05_make_metadata_figure.R │ ├── CTX-M-65-figure-v1 │ │ ├── plot_ctxm65_0diff_subset.html │ │ ├── plot_ctxm65_1diff_subset.html │ │ └── plot_ctxm65_2diff_ctxm14_subset.html │ ├── CTX-M-65-figure-v2 │ │ ├── plot_ctxm65_0diff_subset.html │ │ ├── plot_ctxm65_1diff_ctxm24_subset.html │ │ ├── plot_ctxm65_1diff_subset.html │ │ └── plot_ctxm65_2diff_ctxm14_subset.html │ ├── CTX-M-65-figure │ │ ├── figS1_deduplicated.html │ │ ├── plot_ctxm65_0diff_subset.html │ │ ├── plot_ctxm65_1diff_ctxm24_subset.html │ │ └── plot_ctxm65_2diff_ctxm14_subset.html │ ├── bla-hits-ncbi-analysis.R │ ├── breakpoint_plots │ │ ├── CMY-2_all.html │ │ ├── CMY-2_deduplicated.html │ │ ├── CTX-M-15_all.html │ │ ├── CTX-M-15_deduplicated.html │ │ ├── CTX-M-65_all.html │ │ ├── CTX-M-65_deduplicated.html │ │ ├── GES-1_all.html │ │ ├── GES-1_deduplicated.html │ │ ├── GES-24_all.html │ │ ├── GES-24_deduplicated.html │ │ ├── IMP-4_all.html │ │ ├── IMP-4_deduplicated.html │ │ ├── KPC-2_all.html │ │ ├── KPC-2_deduplicated.html │ │ ├── NDM-1_all.html │ │ ├── NDM-1_deduplicated.html │ │ ├── OXA-10_all.html │ │ ├── OXA-10_deduplicated.html │ │ ├── OXA-48_all.html │ │ ├── OXA-48_deduplicated.html │ │ ├── PER-1_all.html │ │ ├── PER-1_deduplicated.html │ │ ├── TEM-1_all.html │ │ ├── VIM-1_all.html │ │ └── VIM-1_deduplicated.html │ ├── combine-distances-minimap2.py │ ├── correlations_curves.R │ ├── create-subsamples.py │ ├── genes.txt │ ├── gfastats.sh │ ├── gfastats │ │ ├── combined_stats.sh │ │ ├── stats_average_contig_length │ │ ├── stats_bubbles │ │ ├── stats_circular_segments │ │ ├── stats_contig_N50 │ │ ├── stats_contigs │ │ ├── stats_fasta │ │ ├── stats_scaffolds │ │ └── stats_total_contig_length │ ├── make_figures.sh │ ├── output_dist_ctxm.html │ ├── pangraph_statistics.R │ ├── plot-10.html │ ├── plot-100.html │ ├── plot-200.html │ ├── plot-300.html │ ├── plot-400.html │ ├── plot-50.html │ ├── plot_ctxm14.html │ ├── plot_ctxm27.html │ ├── plot_ctxm65.html │ ├── plot_test_10.html │ ├── plot_test_100.html │ ├── plot_test_200.html │ ├── plot_test_50.html │ ├── plot_transposase_density.py │ ├── statistics-summary-table.R │ └── summary_table.tex ├── betalactamases_config.yaml └── data │ ├── BLDB-subset.tsv │ ├── CARD_db.fa │ ├── README.md │ ├── _metadata-preparation │ ├── 01_download-genbank.sh │ ├── 02_get-metadata.py │ ├── 03_extract-xml.py │ ├── 04_combine-metadata.py │ ├── 05a_process-metadata.R │ ├── 05b_process-metadata.R │ └── README.md │ ├── focal_genes.fasta │ └── metadata.csv ├── configs ├── betalactamases_config.yaml ├── cluster_config.yaml ├── config_MCR-1.yaml └── example_config.yaml ├── flanking-regions.yaml ├── manuscript ├── Overleaf │ ├── .gitignore │ ├── cite.bib │ ├── figs_supp │ │ ├── CMY-2.png │ │ ├── CTX-M-15.png │ │ ├── CTX-M-65.png │ │ ├── GES-1.png │ │ ├── IMP-4.png │ │ ├── KPC-2.png │ │ ├── NDM-1.png │ │ ├── OXA-10.png │ │ ├── OXA-48.png │ │ ├── PER-1.png │ │ ├── TEM-1.png │ │ └── VIM-1.png │ ├── main.tex │ └── supplementary.tex ├── README.md ├── figs │ ├── Fig1 │ │ └── Fig1.png │ ├── Fig2 │ │ └── Fig2.png │ ├── Fig3 │ │ └── Fig3.png │ ├── Fig4 │ │ └── Fig4.png │ ├── Fig5 │ │ └── Fig5.png │ ├── Fig6 │ │ └── Fig6.png │ ├── Figure1.pdf │ ├── Figure2.pdf │ ├── Figure3.pdf │ ├── Figure4.pdf │ ├── Figure5.pdf │ └── Figure6.pdf └── supp │ ├── Shaw-Neher-supplementary.pdf │ ├── TableS1.csv │ └── TableS1.xlsx ├── run-pipeline-with-input.py ├── scripts ├── align_central_block.py ├── analyse_promoter_locations.py ├── calculate_AUC.py ├── combine_distances.py ├── combine_fasta_files.py ├── combine_two_plots.R ├── compute_breakpoint_distance_blocks.py ├── compute_distances.py ├── convert_pangraph_to_block_list.py ├── extract_gene_DB.py ├── extract_region_around_gene.py ├── extract_seq_from_fasta.sh ├── install_libraries.R ├── make_pangraph_input_fasta.py ├── make_promotech_script_slurm.py ├── metadata_gene_combinations.py ├── name_variants.py ├── plot_blocks_linear.R ├── plot_entropies.R ├── plot_entropies_cumulative.R ├── plot_linear_blocks_altair.py ├── plot_output_dists.R ├── plot_output_dists_altair.py ├── plot_tree.R ├── plot_tree_variants.R ├── plot_with_gff_annotations.R ├── positional_entropy.py ├── refine_tree.py ├── remove_duplicate_strains.py ├── reverse_complement_gff.py ├── run_promotech_slurm.sh ├── split_fasta.py ├── subset_gff.py └── variants.aln ├── test_data ├── GES-1.fa ├── GES-1_annotations.gff └── GES-1_contigs.fa └── tutorial ├── Tutorial.md └── images ├── ecdf_screenshot.png ├── example_screenshot.png ├── gcp_mcr1_query.png ├── gcp_save_csv.png ├── linear_blocks_screenshot.png ├── mcr1.1_search.png ├── mcr1_search.png └── mcr_salmonella_too_big_flanks.png /.gitignore: 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