Quality control and taxonomic assignation is useful in AMR detection to verify the quality of the data but also to check contamination and confirm species

Time estimation: 2 hours

Learning objectives:

• Run tools to evaluate sequencing data on quality and quantity
• Evaluate the output of quality control tools
• Improve the quality of sequencing data
• Run a series of tool to identify species in bacterial isolate sequencing data
• Visualize the species abundance

• e-learning

  Quality and contamination control in bacterial isolate using Illumina MiSeq Data

  

  • beginner

  Sequence analysis Whole genome sequencing Genomics Microbiology Microbial ecology bacteria illumina microgalaxy

Assembly is a major step in the process of detecting AMR genes as it combines sequenced reads into contigs, longer sequences where it will be easier to identify genes and in particular AMR genes

Time estimation: 4 hours

Learning objectives:

• Run tools to evaluate sequencing data on quality and quantity
• Process the output of quality control tools
• Improve the quality of sequencing data
• Run a tool to assemble a bacterial genome using short reads
• Run tools to assess the quality of an assembly
• Understand the outputs of tools to assess the quality of an assembly
  • Run tools to evaluate sequencing data on quality and quantity
• Process the output of quality control tools
• Improve the quality of sequencing data
• Run a tool to assemble a bacterial genome using short reads
• Run tools to assess the quality of an assembly
• Understand the outputs of tools to assess the quality of an assembly

• e-learning

  Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data

  

  • beginner

  Sequence assembly Whole genome sequencing Public health and epidemiology Genomics Microbiology Assembly assembly illumina microgalaxy
• e-learning

  Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)

  

  • beginner

  Sequence assembly Whole genome sequencing Public health and epidemiology Genomics Microbiology Antimicrobial resistance Assembly amr assembly microgalaxy …

The generated contigs can be annotated to detect genes, potential plasmids, etc. This will help the AMR gene detection process, especially the verification and visualization

Time estimation: 3 hours

Learning objectives:

• Run a series of tool to annotate a draft bacterial genome for different types of genomic components
• Evaluate the annotation
• Process the outputs to formate them for visualization needs
• Visualize a draft bacterial genome and its annotations

• e-learning

  Bacterial Genome Annotation

  

  • beginner

  Genomics Microbiology Gene and protein families Sequence analysis Whole genome sequencing Functional genomics Mobile genetic elements Genome Annotation bacteria gmod …

AMR gene content can be assessed from the contigs to detect known resistance mechanisms and potentially identify novel mechanisms.

Time estimation: 2 hours

Learning objectives:

• Run a series of tool to assess the presence of antimicrobial resistance genes (ARG)
• Get information about ARGs
• Visualize the ARGs and plasmid genes in their genomic context

• e-learning

  Identification of AMR genes in an assembled bacterial genome

  

  • beginner

  Genomics Whole genome sequencing Public health and epidemiology Microbiology Sequence analysis Infectious disease Antimicrobial resistance Genome Annotation amr gmod …

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

• e-learning

  Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

  

  • beginner

  Metagenomics Microbial ecology Public health and epidemiology Taxonomy Sequence assembly Pathology Sequence analysis Heatmap Microbiome Nanopore data analysis …