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