In this post, I compile my notes of the course Metagenomics applied to surveillance of pathogens and antimicrobial resistance. This three-week course is offered by the Technical University of Denmark and is freely accessible at Coursera. As a graduate researcher working on antimicrobial resistance (AMR) in bacterial populations, I have read countless pieces of literature about bacterial population genomics, surveillance and metagenomics in the most recent four years, and I am supposed to be familiar with the content of this course. Nevertheless, the course remains quite helpful to me since it leads me to build a comprehensive knowledge framework of metagenomics from individual concepts. Here, I focus on knowledge that was once unfamiliar or ambiguous to me, and it may be new to some readers as well. More information can be found in course materials on Coursera.