Scripts and accessory data files for: A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation

Maintained by Kristina Ceres: kc649@cornell.edu

Rscripts

• genome_quality_plot.R: quast and checkM results for assembly quality in **Supplemental Figure 1"
• Figure1_plots.R: scripts to create host/geographic distributions and map plot for Figure 1
• get_sample_lineages.R: assign M. bovis clonal complex labels from Zwyer et al.
• PCA.R: Core and accessory genome clustering and plots for Figure 2
• ref_blast_matches.R: analyzing where M. bovis genes identifed by Panaroo map to the M. bovis reference af2122/97
• characterizing_acc_genes.R: plots for Figure 3 related to differnet types of accessory genes
• essential_MTB_genes.R: determining if any pseudogenes were essential in Mtb
• process_Reis_and_Cunha_pangenome: looking at variable genes over the four outbreaks included in the study, and plot for Figure 6

iTOL annotation files

• itol_colorstrip_lineage.txt: Colorstrip file labeling lineages
• ITOL_glpK.txt: heatmap showing presence and absence of glpK 7C-->8C insertion used in Supplemental Figure 4
• ITOL_filtered_genes.txt: presence/absence of filtered accessory genes used in Figure 4
• redundantly_annotated_genes: directory for iTOL gradient files for Supplementary Figure 3

tree files

• unfiltered_acc_gene_dendrogram.nwk: Jaccard distance dendrogram used in Figure2A
• core_genome.final_tree.tre: core phylogeny used in all figures that display core trees
• MN_SNPs.fasta.treefile: SNP tree used for Figure 5
• Glaser_MN_indels.fasta.treefile: indel tree for Figure 5

Parameter_file.md

• parameters for all bioinformatics not conducted in R