Course Overview
Microbes are ubiquitous, living in water, soil, air, and even within the human body. Understanding their genomes is critical for identifying organisms, assessing microbial populations in environmental niches, mapping evolutionary pathways, and determining genetic relatedness among strains. Microbial genomics plays a vital role in modern research, clinical diagnostics, and public health surveillance, particularly for tracking pathogens that rapidly acquire antibiotic resistance.
This course provides a comprehensive, hands-on introduction to Next-Generation Sequencing (NGS) and Whole-Genome Sequencing (WGS) for microbial organisms. Students will learn to process and analyze whole-genome data from bacteria, viruses, archaea, and other microorganisms, identifying genetic variations such as single nucleotide polymorphisms (SNPs), insertions, deletions (indels), and copy number variations. Using practical datasets—such as Staphylococcus aureus genomes—the course demonstrates how to detect variants associated with antibiotic resistance and pathogenicity, providing skills applicable to real-world microbial genomics research.
Course Overview
The program begins with an in-depth introduction to NGS and microbial WGS, explaining the theoretical and practical foundations of variant calling, the significance of haploid versus diploid genomes in microbes, and the biological relevance of mutations. Participants will understand how WGS facilitates the identification of clinically important genetic variants and their implications in microbial resistance.
The course emphasizes hands-on learning using the Snippy pipeline for variant detection. Students will retrieve raw microbial WGS datasets, perform mapping and alignment, call variants, and interpret Variant Call Format (VCF) files. Tools such as Snippy and SnpEff are used for variant effect prediction, allowing participants to link genetic changes to biological functions and disease relevance.
The final sections cover downstream functional analysis, including gene ontology and pathway analysis using tools like topGO, EnrichR, KEGG, PANTHER, and Reactome, enabling students to gain a full understanding of the functional implications of microbial variants. Additional lectures introduce key genomic resources, databases, and file formats commonly used in microbial genomics research, ensuring participants have a solid foundation for independent analysis.
What You'll Learn
- • Fundamentals of NGS and Whole-Genome Sequencing in microbes
- • Identification of SNPs, indels, and other genetic variations
- • Variant calling pipelines using Snippy and SnpEff
- • Interpretation of Variant Call Format (VCF) files
- • Data retrieval, mapping, alignment, and variant detection
- • Functional enrichment analysis and pathway mapping
- • Practical skills for detecting antibiotic resistance and disease-causing mutations
- • Familiarity with genomic databases and file formats (BED, GTF/GFF, SAM/BAM)
- • Linux and command-line tools for microbial genomics
Who Should Enroll
This course is ideal for microbiologists, bioinformaticians, students, and researchers who wish to acquire practical skills in microbial genome analysis, understand variant calling, and apply WGS data for clinical, environmental, or research purposes. No prior experience in NGS or Linux is required.
