Blood faecal genomic comparison

This repository includes the code used to run the analysis in a recent study published in Communications Biology:

Comparative genomics of blood and faecal E. coli and K. pneumoniae isolates from neonates with bloodstream infections in Tanzania Richard N. Goodman, Sabrina J. Moyo, Ilinca Memelis, Aakash Khanijau, Joel Manyahi, Upendo O. Kibwana, Said Aboud, Bjørn Blomberg, Nina Langeland, Adam P. Roberts. Communications Biology 8, 1603 (2025), https://doi.org/10.1038/s42003-025-09008-5

• Figure 1 - ANI and SNP distance matrices
• Figure 2 - core genome phylogenetic tree
• Figure 3 - variant calling heatmaps with breseq
• Figure 4 - circular whole genome comparisons
• Figure 5 - analysing virulence factor determinants