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

new tutorial

Posted on: 26 January 2023 purlPURL: https://gxy.io/GTN:N00043

Food contamination with pathogens are a major burden on our society. Globally, they affect an estimated 600 million people a year and impact socioeconomic development at different levels. These outbreaks are mainly due to Salmonella spp. followed by Campylobacter spp. and Noroviruses.

The evolution of techniques in the last decades has made possible the development of methods to quickly identify responsible pathogen using their DNA and without prior isolation. Long-read sequencing tehcniques like ONT make these methods even easier and more practical to identify strains quicker and with fewer reads.

In this tutorial, using direct Nanopore sequencing data, we show how to

  1. agnostically detect pathogens (what exactly is this pathogen and what is the degree of its severity (its virulence factors) from data extracted directly (without prior cultivation) from a potentially contaminated sample (e.g. food like chicken, cow, etc.,) and sequenced using Nanopore
  2. compare different samples to track the possible source of contamination

This tutorial is offered in 2 different version:

  • A short version, running already build workflows
  • A long version, going step-by-step
View Material

Recent News

See all news

GTN Video Library 2.0: 107 hours of learning across 154 videos

14 June 2024   gtn

Many GTN tutorials already have recordings. These recordings were made by members of the community for a variety of (online) training events. Up until now, this video library were part of the Gallantries Project. We have now integrated this video library directly into the GTN, and made it even easier to add video recordings to GTN tutorials or slide decks! Just use a Google Form to submit your video recordings!

Phylogenetics tutorial takes researchers back to basics!

13 June 2024   Phylogenetics Tutorial GTN Australian BioCommons

A new Galaxy Training Network tutorial has been created to take researchers back to basics to uncover the principles of phylogenetics and how tree-building methods work. A longstanding collaboration between Professor Michael Charleston from the University of Tasmania and Australian BioCommons has delivered this self-guided tutorial featuring videos and hands-on exercises. To maximise its impact, the resource was tailored specifically to be shared globally via the Galaxy Training Network, and will form the basis of an upcoming live training workshop.

From GTN Intern to Tutorial Author to Bioinformatician

13 June 2024   single-cell training education trajectory user contributor

With growing access and interest in sequencing data, Galaxy is a knight in shining armor for wet lab scientists hoping to analyze their own data. With long term intentions of increasing access to bioinformatic analyses, the Galaxy Training Network (GTN) creates a safe space where non-computer-scientists may analyze their own data and even learn to code: an invaluable skill in today’s scientific world. Galaxy introduced me to brand new skills as an undergraduate and ultimately changed the trajectory of my career. Here is my story as a biology undergraduate with no coding experience turned GTN contributor &, eventually, coding bioinformatician: thanks to Galaxy.