Introduction to Microbial Genomics & Metagenomics Training Course

Introduction to Microbial Genomics

• Overview of microbial genomics and metagenomics
• Sequencing technologies and typical study designs
• Key file formats and data organization

Quality Control and Preprocessing

• Read quality assessment and trimming
• Host removal and contamination screening
• Read normalization and downstream considerations

Taxonomic Profiling Approaches

• Marker-based profiling with MetaPhlAn
• K-mer and classification methods with Kraken2 and Bracken
• Comparing profiling outputs and visualization

Metagenome Assembly and Binning (overview)

• Assembly strategies and SPAdes usage
• Contig binning concepts and common tools (brief)
• Assessing assembly quality and completeness

Genome Annotation and MLST

• Annotating genomes with Prokka
• Performing MLST and interpreting sequence types
• Generating reports for sharing results

SNP Calling and Phylogenetics

• Mapping-based SNP calling workflows with Snippy
• Building phylogenetic trees with IQ-TREE
• Tree visualization and interpretation with iTOL

Antimicrobial Resistance and Functional Profiling

• AMR gene detection with AMRFinderPlus, CARD, and ResFinder
• Functional profiling and pathway summaries
• Reporting resistance and functional annotations

Reproducible Workflows and Best Practices

• Using Conda, Docker, and pipeline templates for reproducibility
• Data management, metadata standards, and FAIR principles
• Scaling analyses with cloud resources and notebooks

Case Studies and Hands-on Labs

• 16S/18S amplicon analysis from raw reads to taxonomic table
• Metagenomic profiling and comparative analysis across samples
• Genome assembly, annotation, SNP phylogeny, and AMR reporting

Summary and Next Steps