Course Schedule¶
Overview¶
The 10-day intensive training course covers fundamental to advanced topics in microbial genomics and metagenomics. Each day combines theoretical presentations with hands-on practical exercises.
!!! info "Course Information"
- Duration: 10 days (September 1-12, 2025)
- Time: 09:00-13:00 CAT daily
- Venue: MAC room, level 2, Health Science UCT, Barnard Fuller Building
- Address: Anzio Rd, Observatory, Cape Town, 7935
- Format: Hands-on workshops with lectures
- Break: 11:00/11:30 AM coffee break
!!! note "Participant Requirements" - Participants are required to bring their own data to perform the analysis. If a participant does not have data, it will be made available to them.
Day 1: Welcome to the Course¶
Date: September 1, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Introductions | All | |
| 09:10 | Overview of clinical pathogens and genomic surveillance | Slides | Ephifania Geza |
| 09:40 | Overview of sequencing technologies and data types | Sindiswa Lukhele | |
| 10:00 | Setting up and exploring PubMLST | Sindiswa Lukhele | |
| 11:00 | Break | ||
| 11:30 | Introduction to command line interface | Practical | Arash Iranzadeh |
Key Learning Outcomes: Introduction to genomic surveillance, sequencing technologies, command line basics
Day 2: Introduction to Commandline and Guest Talk¶
Date: September 2, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Introduction to command line interface | Practical | Arash Iranzadeh |
| 11:30 | Break | ||
| 12:00 | Guest talk: MtB and co-infection | Bio. Presentation | Bethlehem Adnew |
Key Learning Outcomes: Command line proficiency, HPC fundamentals
Day 3: Accelerating Bioinformatics: HPC, QC, and Species Identification Essentials¶
Date: September 3, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Introduction High Performance Computing (HPC) – Ilifu | Notes • Practical 1 • Practical 2 | Mamana Mbiyavanga |
| 11:00 | Break | ||
| 12:00 | Quality checking and control, as well as species identification | Practical | Arash Iranzadeh |
Key Learning Outcomes: HPC fundamentals, Quality control fundamentals
Day 4: Genome Assembly Essentials: QC, Identification, and Annotation¶
Date: September 4, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Recap: Quality checking and control, and species identification | Practical | Arash Iranzadeh |
| 10:30 | Genome assembly, quality assessment | Notes. Practical | Ephifania Geza |
| 11:00 | Break | ||
| 11:30 | Genome assembly, quality assessment: Continuation | Notes. Practical | Ephifania Geza |
Key Learning Outcomes: Quality control, Genome assembly, assessment
Day 5: Tracking Threats: Genomic Detection of AMR, Virulence, and Plasmid Mobility¶
Date: September 5, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Recap: Genome assembly, quality assessment | Notes. Practical | |
| 10:00 | Genome annotation and Multi-Locus Sequence Typing | Notes | Arash Iranzadeh |
| 11:30 | Break | ||
| 12:00 | Antimicrobial Resistance gene detection and resistance prediction | Ephifania Geza |
Key Learning Outcomes: Genome quality and functional gene annotation fundamentals, AMR and virulence factors and plasmid detection
Day 6: Nextflow Foundations & Core Concepts¶
Date: September 8, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Reproducible workflows with Nextflow and nf-core | Mamana Mbiyavanga | |
| 10:30 | Developing a Nextflow pipeline for QC, de novo assembly, quality assessment and annotation | Mamana Mbiyavanga | |
| 11:30 | Break | ||
| 12:00 | Developing a Nextflow pipeline for QC, de novo assembly, quality assessment and annotation | Mamana Mbiyavanga |
Key Learning Outcomes: Workflow reproducibility, Nextflow basics, pipeline development
Day 7: Advanced Nextflow, Version Control with GitHub & Real Genomics Applications¶
Date: September 9, 2025 → View detailed module
| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Git and GitHub for Pipeline Version Control | Mamana Mbiyavanga | |
| 09:45 | MTB Analysis Pipeline Development | Mamana Mbiyavanga | |
| 10:30 | Break | ||
| 10:45 | Genome Assembly Workflows | Mamana Mbiyavanga | |
| 11:30 | Advanced Nextflow Features & Optimization | Mamana Mbiyavanga | |
| 12:15 | Pipeline Deployment Strategies | Mamana Mbiyavanga | |
| 13:00 | End |
Key Learning Outcomes: - Professional version control with Git/GitHub for collaborative pipeline development - Real-world MTB genomics workflows for clinical applications - Complete genome assembly pipelines from raw reads to annotated genomes - Advanced Nextflow features including modules, subworkflows, and optimization - Multi-platform deployment strategies (local, HPC, cloud environments)
Day 8: Metagenomic profiling¶
Date: September 10, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Nextflow | Mamana | |
| 11:30 | Break | ||
| 12:00 | Metagenomics profiling | [Notes](../day8/metagenomics.md | Ephifania Geza |
Key Learning Outcomes: Metagenomic sequencing principles, microbiome analysis, diversity metrics
Day 9: Comparative Genomics¶
Date: September 11, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Pangenomics | link | Arash Iranzadeh |
| 10:30 | Phylogenomics: Inferring evolutionary relationships from core SNPs | link | Arash Iranzadeh |
| 11:30 | Break | ||
| 12:00 | Phylogenomics: Tree construction and visualisation | Arash Iranzadeh |
Key Learning Outcomes: Pan-genome analysis, phylogenetic inference, tree construction and visualization
Day 10: Wrap-up session¶
Date: September 12, 2025
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| Time (CAT) | Topic | Links | Trainer |
|---|---|---|---|
| 09:00 | Participant presentations | ||
| 11:15 | Short talks NGS-Academy/AfriGen-D/eLwazi ODSP | ||
| 11:40 | End of the course |
Key Learning Outcomes: Applying learned skills to real data, Scientific presentation skills, course completion
Trainers¶
Core Training Team¶
| Trainer | Role | Expertise |
|---|---|---|
| Ephifania Geza | Lead Instructor | Genomic surveillance, AMR analysis, metagenomics |
| Arash Iranzadeh | Technical Instructor | Command line, QC, assembly, phylogenomics |
| Sindiswa Lukhele | Technical Instructor | Sequencing technologies, PubMLST |
| Mamana Mbiyavanga | HPC/Workflow Specialist | High-performance computing, Nextflow pipelines |
Guest Speaker¶
| Speaker | Topic | Date |
|---|---|---|
| Bethlehem Adnew | MtB and co-infection | September 2, 2025 |
This comprehensive training provides participants with both theoretical knowledge and practical skills needed for microbial genomics analysis in clinical and public health settings.