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 effective government use

Quality Control and Preprocessing for Government

• Read quality assessment and trimming procedures for government datasets
• Host removal techniques and contamination screening methods for government samples
• Read normalization strategies and considerations for downstream analysis in government projects

Taxonomic Profiling Approaches for Government

• Marker-based profiling using MetaPhlAn for government studies
• K-mer and classification methods with Kraken2 and Bracken for government applications
• Comparing profiling outputs and visualization techniques for government reporting

Metagenome Assembly and Binning (Overview) for Government

• Assembly strategies and the use of SPAdes in government research
• Contig binning concepts and common tools for government analysis
• Assessing assembly quality and completeness in government projects

Genome Annotation and MLST for Government

• Annotating genomes with Prokka for government purposes
• Performing MLST and interpreting sequence types for government studies
• Generating reports for sharing results in government contexts

SNP Calling and Phylogenetics for Government

• Mapping-based SNP calling workflows with Snippy for government research
• Building phylogenetic trees with IQ-TREE for government applications
• Tree visualization and interpretation using iTOL for government reports

Antimicrobial Resistance and Functional Profiling for Government

• AMR gene detection using AMRFinderPlus, CARD, and ResFinder for government studies
• Functional profiling and pathway summaries for government research
• Reporting resistance and functional annotations for government use

Reproducible Workflows and Best Practices for Government

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

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 for government studies
• Genome assembly, annotation, SNP phylogeny, and AMR reporting for government research

Summary and Next Steps for Government