CPG bioinformatics workshop Nepal - Feb 2026

Centre for Pathogen Genomics (CPG), The University of Melbourne

This hands-on training focuses on analysing Oxford Nanopore Technologies (ONT) sequencing data for microbial pathogen detection. Participants will learn how to process and analyse nanopore sequencing data using web-based (Galaxy/CPG Portal) and command-line interface (CLI) tools.

Prerequisites

• Basic understanding of molecular biology and microbiology
• Access to a computer with an internet connection
• Familiarity with command-line interface (helpful but not required)

Learning Objectives

By the end of this training, participants will be able to:

• Understand the use of Galaxy and CPG Portal for bioinformatics analyses
• Understand the basics of using the command-line interface (CLI)

• Understand the bioinformatics workflow for pathogen detection using nanopore sequencing data

  • Perform quality control and preprocessing of nanopore reads
  • Perform taxonomic profiling to identify pathogens
  • Optional: Assemble bacterial genomes from processed nanopore reads
  • Optional: Detect antimicrobial resistance (AMR) genes

Requirements - please set up before the training 🗂️🛠️

Before the start of the course, please create an account for the following web services (free):

• Galaxy Click the Register here button at the bottom
• CPG Portal Click the Sign Up button on the top right

If you want to use command-line tools, please ensure you have access to a Unix-based system (Linux or MacOS) or install WSL2 on Windows. Additionally, install conda for package management.

1. Install WSL (Windows users): Follow WSL installation guide
2. Setup Conda Environment: Follow conda setup guide
3. Download data and databases: Follow Data download guide

Precourse material - read/watch at your leisure

Training material for pathogen detection using nanopore reads

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

Optional Videos to watch before the course starts:

• A brief history of Computational Biology and Sequencing
• Introduction to Galaxy
• Galaxy training - Pathogen detection from nanopore sequencing data

Optional Publication to read:

• Twenty years of bacterial genome sequencing - Discusses the history of sequencing technology
• So you want to be a computational biologist? - Advice by two bioinformaticians

Workshop schedule/materials

1. Introduction to Galaxy for Bioinformatics
2. Basic Linux command-line skills for bioinformatics
3. QC, data preprocessing, and taxonomic profiling of nanopore sequencing data
4. Genome assembly and polishing of bacterial genomes from nanopore data
5. AMR profiling from genome assemblies

Training lecture zoom sessions - NPHL (11-16th Feb)

Join from PC, Mac, iOS or Android: zoom link Password: 052674

Download full program schedule here

CPG ONT QC guidelines

1. Setting up your PC for ONT QC analysis
2. Running ONT QC with the CPG guidelines

Acknowledgments

• Centre for Pathogen Genomics (CPG), MDU-PHL, and The University of Melbourne for funding and supporting this training
• Galaxy Training Network for the training materials
• Kathmandu University, Shubham Biotech Nepal, and National Public Health Laboratory, Nepal as partners in delivering this training
• All contributors and participants

Happy Learning! 🧬🔬💻

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License

This training material is licensed under CC BY 4.0.