rngoodman/blood-faecal-genomic-comparison

Code for paper which ran a genomic comparison of blood and faecal isolates from the same neonatal patients hospitalised with fever in Dar es Salaam, Tanzania # 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), doi.org * 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