Microbial Genomics
I Introduction
Workshop Info
Pre-work
Schedule
AWS Setup Instructions
Meet Your Faculty
Data and Compute Setup
II Modules
Module 1 Microbial Genome Sequencing
Lecture
Module 2 Genome Assembly and Annotation
Lecture
Lab
Module 3 Mobile Genetic Elements
Lecture
Lab
Contents
Overview
Dataset
Part 1: MOB-suite
Part 2: IslandCompare
Part 3: Microreact
References
Appendix
IslandCompare Data Download
Microreact Data Download
Module 4 Antimicrobial Resistant Gene (AMR) Analysis
Lecture
Lab
Download Files
Introduction
CARD Website and Antibiotic Resistance Ontology
RGI for Genome Analysis
RGI at the Command Line
RGI for Merged Metagenomic Reads
Metagenomic Sequencing Reads and the KMA Algorithm
Module 5 Pan Genomics
Lecture
Lab
Introduction
Learning Objectives
Environment Setup
Part 1: Understanding the structural layout of cDBGs
Part 2: Annotating and interpreting a pangenome graph
Part 3: Impact of k-mer length on graph topology
Wrap-Up
Module 6 Phylogenetics
Lecture
Sponsors
Microbial Genomics 2025
Module 6 Phylogenetics
Lecture