Scripts that have helped with analysis
gc_content.py
Calculated gc content, gc count, N count, sequence length for all contigs and for contigs greater than 500b.p.
snpable_pos_3.py
From an alignment see which isolates have an N at a specific loci where other isolates collectively have 2 or more of the following bases: A,T,C,G.
Useful for looking into alignments from snapperDB v2.
python3 snpable_pos_3.py -a test_snpable_data.fa -p 10
ggtree_vir_heatmap.R
Using R to add virulence data to better annotate a phylogenetic tree.