Workshops and courses

A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy

View event

Date: 14 October 2025 @ 09:00 - 17:00

Language of instruction: English

Loading map...

The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. The workshop will be on October 14th 2024 as a 1-day F2F at FHNW Muttenz, Switzerland, free and practical workshop.

Keywords: foodborne, introduction, metagenomics, sequence-analysis

Venue: FHNW University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 30

City: Muttenz

Country: Switzerland

Postcode: 4132

Learning objectives:

  • Check quality reports generated by FastQC and NanoPlot for metagenomics Nanopore data
  • Familiarize yourself with the basics of Galaxy
  • 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
  • Learn how histories work
  • Learn how to create a workflow
  • Learn how to obtain data from external sources
  • Learn how to run tools
  • Learn how to share your work
  • 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
  • Relate all samples' pathogenic genes for tracking pathogens via phylogenetic trees and heatmaps

Organizer: Abdullah Kahraman (https://training.galaxyproject.org/training-material/hall-of-fame/abdullahkahraman/), Anna Henger (https://training.galaxyproject.org/training-material/hall-of-fame/annahenger/)

Event types:

  • Workshops and courses

Instructors: Wolfgang Maier, Engy Nasr, Santino Faack

Scientific topics: Metagenomics, Public health and epidemiology, Taxonomy, Sequence assembly, Pathology, Sequence analysis

Activity log