hands-on tutorial
Hands-on for 'Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition' tutorial
The questions this addresses are:
- What are the preprocessing steps to prepare ONT sequencing data for further analysis?
- How to identify pathogens using sequencing data?
- How to track the found pathogens through all your samples datasets?
The objectives are:
- 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
Licence: Creative Commons Attribution 4.0 International
Keywords: metagenomics, Nanopore data analysis, Pathogens detection, Phylogenetic tree, Heatmap, cyoa
Target audience: Students
Resource type: hands-on tutorial
Scientific topics: Metagenomics
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