Keywords: amr, bacteria, microgalaxy, one-health

Learning objectives:

• Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data
• Evaluate the annotation
• Evaluate the output of quality control tools
• Get information about ARGs
• 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
• Improve the quality of sequencing data
• Perform taxonomy profiling indicating and visualizing up to species level in the samples
• Preprocess the sequencing data to remove adapters, poor quality base content and host/contaminating reads
• Process the output of quality control tools
• Process the outputs to formate them for visualization needs
• Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps
• Run a series of tool to annotate a draft bacterial genome for different types of genomic components
• Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)
• Run a series of tool to identify species in bacterial isolate sequencing data
• Run a tool to assemble a bacterial genome using short reads
• Run tools to assess the quality of an assembly
• Run tools to evaluate sequencing data on quality and quantity
• Understand the outputs of tools to assess the quality of an assembly
• Visualize a draft bacterial genome and its annotations
• Visualize the ARGs and plasmid genes in their genomic context
• Visualize the species abundance

Event types:

• Workshops and courses

Sponsors: ABRomics, Avans Hogeschool, ELIXIR Europe, Institut Français de Bioinformatique

Scientific topics: Whole genome sequencing, Genomics, Microbiology, Microbial ecology, Sequence assembly, Public health and epidemiology, Antimicrobial resistance, Gene and protein families, Sequence analysis, Functional genomics, Mobile genetic elements, Infectious disease, Metagenomics, Taxonomy, Pathology