The Guide
Welcome to the MicroGen 2026 workshop!
This workshop is designed to equip you with the essential computational skills needed for microbial genomics and bioinformatics.
Over the next four days, we will journey from the basics of the Linux computing environment to advanced phylogenetic analysis and metagenomics, while also applying our learning to real-world study cases in infectious diseases.
What to expect
- Day 0 - Pre-workshop: Setting up your computational environment and getting comfortable with the Linux environment and command lines.
- Day 1: Introduction to whole-genome sequencing and genome assembly.
- Day 2: Assembly and gene-level analysis. Long-read sequencing.
- Day 3: Core SNP and phylogenetic analysis.
- Day 4: Read-based metagenomic analysis for AMR surveillance and actionable clinical diagnosis.
Prerequisites
This workshop is suitable for participants with little to no prior experience in bioinformatics. However, a basic understanding of clinical microbiology and molecular biology will be beneficial. No prior programming experience is required, as we will start from the fundamentals.
How to use this guide
Each day is divided into several modules, each focusing on a specific topic. Each module includes:
- Introduction: A brief overview of the topic.
- Guided analyses: Practical tasks to analyse specific real-world datasets.
- Code blocks: Commands and scripts to run the analyses.
- Challenges: Optional advanced tasks to sharpen your skills.
- Self exploration: Suggestions for further exploration of more advanced analysis techniques and tools.
We encourage you to try the challenges and self exploration sections. Be confident to ask questions and help each other. The goal is to learn by doing!