Beginner Course on Microbial Genomics:
Applications & Research
A bioinformatics workshop organised by the Molecular Epidemiology Group at Oxford University Clinical Research Unit in May, 2026.
This workshop is a part of the KLEB-CASAVA project, funded by the UKRI.
Aiming to enhance the local capacity in genomic epidemiology and surveillance, the workshop provides essential bioinformatics skills for Vietnamese clinicians and researchers, whose work focuses on bacterial infectious diseases, but have little to no experience in analysing whole-genome sequencing data.
Programme
Pack your backpack
Setting up your computational environment and getting comfortable with the Linux environment and command lines.
Slides | Practical Guides | Data
Module 0.1: Setup your workspace
Module 0.2: Commands & Environments
Meet the genomes
Introduction to whole-genome sequencing and genome assembly.
Slides | Practical Guides | Data
Module 1.1: Whole-genome sequencing - What? & Why?
Module 1.2: A complete genome - How it look like?
Module 1.3: From raw sequencing data to assemblies
Inspect the genomes
Assembly and gene-level analysis. Long-read sequencing.
Slides | Practical Guides | Data
Module 2.1: Analyse the assemblies
Module 2.2: Long-read sequencing & Hybrid assemblies
Module 2.3: Locate & compare genes
Phylogenetics - Relationships between genomes
Core SNP and phylogenetic analysis.
Slides | Practical Guides | Data
Module 3.1: Read mapping & SNP alignment
Module 3.2: Phylogenetic tree inference
Metagenomics
Read-based metagenomic analysis for AMR surveillance and actionable clinical diagnosis.
Slides | Practical Guides | Data
Module 4.1: Clinical foundations & AMR surveillance: workflow setup
Module 4.2: Vietnamese healthy gut microbiome: taxonomy analysis
Module 4.3: Vietnamese healthy gut microbiome: AMR analysis and summary
Module 4.4: Actionable diagnostics & clinical reasoning: case simulation
Module 4.5: Actionable diagnostics & clinical reasoning: signal analysis
Instructors
Dr. Pham Thanh Duy
Head of Molecular Epidemiology Group
Center for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University
Dr. Chung The Hao
Senior Postdoc Fellow
Saw Swee Hock School of Public Health, National University of Singapore
Acknowledgement
