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Course Overview

About the Course

This comprehensive 10-day training course introduces participants to the core principles and practical applications of microbial genomics and metagenomics in clinical and public health contexts.

Course Schedule (September 1-12, 2025)

The training covers 10 days of intensive hands-on learning:

Week 1: Foundations

  • Day 1: Course welcome, genomic surveillance, sequencing technologies, PubMLST
  • Day 2: HPC introduction, command line, quality control, species identification
  • Day 3: Genome assembly, annotation, MLST, serotyping, AMR detection
  • Day 4: Comparative genomics, pangenomics, phylogenomics
  • Day 5: Metagenomic profiling and microbiome analysis

Week 2: Advanced Applications

  • Day 6: Co-infection detection, variant calling, genotype-phenotype correlation
  • Day 7: Nextflow workflow development and nf-core
  • Day 8: Advanced pipeline development and optimization
  • Day 9: Bring-your-own-data analysis session
  • Day 10: Final presentations and course wrap-up

Target Pathogens

Using real-world datasets, participants will analyze:

  • Mycobacterium tuberculosis - TB genomics and drug resistance analysis
  • Vibrio cholerae - Outbreak investigation and epidemiological analysis

Key Focus Areas

Genomic 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

  • Master version control with Git
  • Work with containerized environments (Docker/Singularity)
  • Implement Nextflow pipelines for scalable analysis

Course Format

  • Interactive workshops with hands-on exercises
  • Real-world datasets from clinical and surveillance studies
  • Expert instruction from experienced genomics researchers
  • Group projects and individual presentations
  • Bring-your-own-data analysis sessions

Expected Outcomes

By the end of this course, participants will be equipped with practical skills to conduct genomic surveillance, investigate outbreaks, and contribute to public health decision-making through genomic analysis.