Day 3: Phylogenetics - Relationships between genomes

At this stage, we’re gonna learn how to compare and infer the evolutionary relationships between the outbreak’s isolates from their short-read sequencing data. These analyses will enable us to answer questions, such as:

• Are the outbreak isolates genomically related to each other?
• How many transmission events occurred during the outbreak?
• What is the direction of transmission?
• How does the outbreak spread in the hospital?
• How does the pathogen evolve during the outbreak?
• What could be the origin of the outbreak?

We will journey through the following topics:

1. Genome mapping: How to map sequencing reads of the outbreak’s isolates to a reference genome.
2. SNP calling & alignment: How to identify single-nucleotide polymorphisms (SNPs) among the outbreak’s isolates.
3. Phylogenetic tree inference: How to infer genomic relatedness between the outbreak’s isolates.

Now, let’s begin!