Day 2: Inspect the genomes

Following Day 1, on this day, we’re gonna learn how to analyse the genome assemblies to investigate the genomic features of the outbreak’s isolates, such as their multi-locus sequence type (MLST), antimicrobial resistance genes, virulence factors, and other genomic features.

We will journey through the following topics:

1. Assembly quality control: How to assess the quality of the de novo assemblies.
2. Species identification and MLST typing: How to identify the species and strain of bacteria.
3. AMR gene profiling: How to identify antimicrobial resistance genes.
4. Long-read sequencing & Hybrid assembly: How to use long-read sequencing data to improve genome assembly.
5. Genome annotation: How to annotate the genome with functional information.
6. Gene variation analysis: How to identify gene variations between isolates.

Now, let’s get started!