Blood faecal genomic comparison

This repository includes the code used to run the analysis in a recent study currently posted as a preprint on bioRxiv:

Goodman, R.N., Moyo, S.J., Memelis, I., Khanijau, A., Manyahi, J., Kibwana, U.O., Aboud, S., Blomberg, B., Langeland, N. & Roberts, A.P. (2025) Genomic comparison of highly related pairs of E. coli and K. pneumoniae isolated from faeces and blood of the same neonatal patients hospitalized with fever in Dar es Salaam, Tanzania. bioRxiv. doi:10.1101/2025.04.28.650962.

• 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