Introduction to Microbial Genomics & Metagenomics Training Course

Introduction to Microbial Genomics for Government

• Overview of microbial genomics and metagenomics for government applications
• Sequencing technologies and typical study designs for government research
• Key file formats and data organization for efficient government workflows

Quality Control and Preprocessing for Government

• Read quality assessment and trimming to ensure data integrity for government projects
• Host removal and contamination screening to maintain accuracy in government studies
• Read normalization and downstream considerations for robust government analyses

Taxonomic Profiling Approaches for Government

• Marker-based profiling with MetaPhlAn for accurate taxonomic identification in government research
• K-mer and classification methods with Kraken2 and Bracken to enhance government data analysis
• Comparing profiling outputs and visualization techniques for clear communication in government reports

Metagenome Assembly and Binning (Overview) for Government

• Assembly strategies and SPAdes usage to optimize metagenome assembly for government projects
• Contig binning concepts and common tools to support comprehensive government research
• Assessing assembly quality and completeness to ensure reliable results in government studies

Genome Annotation and MLST for Government

• Annotating genomes with Prokka for detailed genome characterization in government research
• Performing MLST and interpreting sequence types to support government epidemiological studies
• Generating reports for sharing results within government agencies

SNP Calling and Phylogenetics for Government

• Mapping-based SNP calling workflows with Snippy to support genetic analysis in government projects
• Building phylogenetic trees with IQ-TREE to enhance evolutionary understanding in government research
• Tree visualization and interpretation with iTOL for clear presentation of findings in government reports

Antimicrobial Resistance and Functional Profiling for Government

• AMR gene detection with AMRFinderPlus, CARD, and ResFinder to support public health initiatives in government
• Functional profiling and pathway summaries to enhance biological insights in government studies
• Reporting resistance and functional annotations to inform policy decisions in government

Reproducible Workflows and Best Practices for Government

• Using Conda, Docker, and pipeline templates for reproducibility in government research
• Data management, metadata standards, and FAIR principles to ensure transparency in government projects
• Scaling analyses with cloud resources and notebooks to support large-scale government initiatives

Case Studies and Hands-on Labs for Government

• 16S/18S amplicon analysis from raw reads to taxonomic table for government applications
• Metagenomic profiling and comparative analysis across samples in government studies
• Genome assembly, annotation, SNP phylogeny, and AMR reporting for comprehensive government research

Summary and Next Steps for Government