Time estimation: 4 hours

Learning objectives:

• Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data
• Preprocess the sequencing data to remove adapters, poor quality base content and host/contaminating reads
• Perform taxonomy profiling indicating and visualizing up to species level in the samples
• Identify pathogens based on the found virulence factor gene products via assembly, identify strains and indicate all antimicrobial resistance genes in samples
• Identify pathogens via SNP calling and build the consensus gemone of the samples
• Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps