Centre for Research Informatics Training
Working with bacterial genomes
Event details
Sessions
- 18 May 2027 — 09:30 to 17:30 — Craik-Marshall
- 19 May 2027 — 09:30 to 17:30 — Craik-Marshall
- 20 May 2027 — 09:30 to 17:30 — Craik-Marshall
- 21 May 2027 — 09:30 to 17:30 — Craik-Marshall
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About the course
Bacterial genomics has become an essential approach for studying microbial diversity, evolution, epidemiology, and antimicrobial resistance. This course provides a practical introduction to analysing bacterial genomes, primarily using Illumina-sequenced samples.
Participants will learn how to select appropriate analysis strategies based on the genomic diversity of different bacterial species and will gain hands-on experience using both de novo assembly and reference-based mapping approaches to reconstruct bacterial genomes. The course covers standardised workflows for genome assembly and annotation, together with approaches for assessing the quality of assembled genomes.
Participants will also learn methods for bacterial typing, including MLST, cgMLST, and PopPUNK, and will construct phylogenetic trees using whole genome and core genome alignments. The course further covers methods for estimating time-scaled phylogenies and detecting antimicrobial resistance genes using a range of species-specific and general-purpose tools.
Examples throughout the course are drawn from Mycobacterium tuberculosis, Staphylococcus aureus, and Streptococcus pneumoniae, providing participants with practical experience that can be applied across a range of bacterial species.
By the end of the course, participants should be able to conduct bacterial genomics analyses from raw sequencing data through to phylogenetic interpretation and antimicrobial resistance profiling.
Teaching is primarily hands-on, with short presentations and demonstrations introducing the concepts and methods needed to analyse bacterial genomic data.
Intended audience
This course is suitable for:
- biologists interested in microbiology and prokaryotic genomics
- researchers interested in antimicrobial resistance and pathogen surveillance
- participants who want practical experience with bacterial genomics analysis workflows
- researchers seeking to apply genomic approaches to the study of bacterial evolution and epidemiology
Prerequisites
Participants should have:
- a basic understanding of high-throughput sequencing technologies
- a working knowledge of the UNIX command line
- a working knowledge of R
The following experience is recommended:
- a basic knowledge of phylogenetic inference methods
- running analyses on High Performance Computing (HPC) clusters
Course fees
All fees are per full training day.
| Category | Fee |
|---|---|
| Industry full charge | £130.00 |
| Academic / Government / charity concessionary | £65.00 |
| Cambridge University staff members / postdocs / visitors | £65.00 |
| Cambridge University registered students | Free |
| Cambridge University registered students non-attendance | £22.00 |
| Special events | Per event |
Payment options will be provided in booking confirmation emails sent after registration.
General information
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