Microbial Genomics & Metagenomics Training¶
Welcome to the comprehensive training course on Microbial Genomics & Metagenomics for Clinical and Public Health Applications.
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Course Overview
Learn core principles and practical applications of microbial genomics and metagenomics in clinical and public health contexts.
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10-Day Program
Intensive hands-on training covering everything from command line basics to advanced outbreak investigation.
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Real-World Data
Work with actual clinical datasets including M. tuberculosis and V. cholerae.
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Practical Skills
Master bioinformatics tools, workflows, and reproducible analysis techniques used in clinical microbiology.
What You'll Learn¶
This course provides hands-on experience with:
Pathogen Analysis¶
- Analyze genomic diversity and evolutionary relationships
- Investigate antimicrobial resistance (AMR) profiles
- Study mobile genetic elements (MGE) in resistance spread
Metagenomics¶
- Explore microbial communities in clinical and environmental samples
- Apply advanced sequencing analysis techniques
- Interpret complex metagenomic datasets
Reproducible Workflows¶
- Use version control with Git
- Work with containerized environments
- Implement Nextflow pipelines for scalable analysis
Data Interpretation¶
- Generate publication-ready visualizations
- Conduct epidemiological investigations
- Present findings effectively
Course Highlights¶
Interactive Learning
- Hands-on exercises with real datasets
- Group discussions and case studies
- Individual project presentations
- Expert guest speakers
Technical Requirements
- Laptop (Linux/macOS preferred, Git Bash for Windows)
- Basic Linux command-line knowledge
- HPC access (recommended)
Getting Started¶
Ready to begin your journey in microbial genomics? Start with our setup guide:
Course Information¶
| Duration | 10 days (September 1-12, 2025) | | Format | Hands-on workshops with lectures | | Level | Intermediate | | Prerequisites | Basic bioinformatics knowledge |
Support¶
Need help? Check our troubleshooting guide or reach out to the course instructors.
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Repository
Access all course materials, datasets, and workflows on GitHub.
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Documentation
Comprehensive guides, references, and additional resources.