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 strategies.

Quality Control and Preprocessing

• Read quality assessment and trimming techniques.
• Host genome removal and contamination screening.
• Read normalization and considerations for downstream analysis.

Taxonomic Profiling Approaches

• Marker-based profiling using MetaPhlAn.
• K-mer and classification methods utilizing Kraken2 and Bracken.
• Comparing profiling outputs and visualization techniques.

Metagenome Assembly and Binning (Overview)

• Assembly strategies and usage of SPAdes.
• Concepts of contig binning and an overview of common tools.
• Assessing assembly quality and completeness.

Genome Annotation and MLST

• Genome annotation using Prokka.
• Performing Multi-Locus Sequence Typing (MLST) and interpreting sequence types.
• Generating reports for sharing results.

SNP Calling and Phylogenetics

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

Antimicrobial Resistance and Functional Profiling

• Detection of AMR genes using AMRFinderPlus, CARD, and ResFinder.
• Functional profiling and pathway summaries.
• Reporting resistance and functional annotations.

Reproducible Workflows and Best Practices

• Utilizing 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 tables.
• Metagenomic profiling and comparative analysis across samples.
• Genome assembly, annotation, SNP phylogeny, and AMR reporting.

Summary and Next Steps