Haplotype-based methods for efficient detection of recombinogenic pathogen lineages at scale

Whole-genome sequencing of bacterial lineages with recombination is becoming increasingly widespread and is crucial for understanding genetic diversity, disease transmission, and evolutionary processes. In my project, I will be working on the problem of developing scalable, haplotype-based approaches to identify sections of DNA inherited through recombination. This is done through local ancestry analysis where different sections of the genome have their own ancestry tree and therefore, we analysis the ancestry of a sequence of trees across the genome. The goal is to build a more efficient early warning system for emerging bacterial lineages of concern, for example ones created from the recombination of anti-microbial resistant and virulent lineages. By improving detection speed and accuracy, the system would enable faster public health responses and more timely intervention measures to mitigate the impact of these pathogens.