CIDRI-Africa/microbial-genomics-training

A hands-on training course that introduces participants to the core principles and practical applications of microbial genomics and metagenomics in clinical and public health contexts. Participants will learn how to characterize clinically significant pathogens: M. tuberculosis, V. cholerae, E. coli, and S. sonnei. # Microbial Genomics & Metagenomics Training Course [ ] ## 🔬 Course Overview This comprehensive 10-day intensive training course introduces participants to the core principles and practical applications of microbial genomics and metagenomics in clinical and public health contexts. Using real-world datasets and reproducible workflows, participants will learn to analyze genomic diversity, evolutionary relationships, and antimicrobial resistance (AMR) profiles of clinically significant pathogens. ## 🎯 Target Pathogens - **_Mycobacterium tuberculosis_** - Drug resistance and transmission dynamics - **_Vibrio cholerae_** - Outbreak investigation and epidemic analysis ## 📅 Course Information - **Dates**: September 1-12, 2025 - **Time**: 09:00-13:00 CAT daily - **Duration**: 10 days intensive training - **Venue**: MAC room, level 2, Health Science UCT, Barnard Fuller Building - **Address**: Anzio Rd, Observatory, Cape Town, 7935 - **Format**: Hands-on workshops with lectures ## 🎓 Learning Outcomes After completing this course, participants will be able to: - **Understand** the principles of pathogen genomics and its role in infectious disease surveillance and control - **Describe** the workflow of genomic data generation, from sample collection to sequence analysis - **Apply** bioinformatics tools to analyze pathogen genomic data - **Interpret** genomic data for epidemiological insights, including outbreak detection and tracking - **Understand** the role of genomics in identifying antimicrobial resistance mechanisms - **Implement** reproducible analysis workflows using modern tools and best practices ## 📚 Course Structure ### Week 1: Foundations (Days 1-5) - **Day 1**: Introduction and genomic surveillance overview - **Day 2**: Command line, HPC, and quality control - **Day 3**: Genomic characterization and assembly - **Day 4**: Comparative genomics and phylogenetics - **Day 5**: Metagenomic profiling ### Week 2: Advanced Applications (Days 6-10) - **Day 6* …