GenEpi-BioTrain - Virtual training 17 - Nanopore Sequencing Technology

Topic outline

• Nanopore Sequencing Technology (GenEpi-BioTrain — Virtual Training 17)

  Nanopore Sequencing Technology (GenEpi-BioTrain — Virtual Training 17)

  ℹ️ Please Note

  You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 17 held April 2025, and certificates are only issued to participants who attended the live webinar sessions.

  Welcome to this virtual training space on the Learning Portal.

  Below you will see the two online sessions and their support materials.

  In anticipation for the live sessions, we encourage participants to:

  1. Explore the materials available; 

  2. Install the software indicated below;

  3. Suggest topics of interest for future virtual trainings

  • The practical exercise in this webinar has several 'Pre-requisites' and 'Software requirements'. Please read them carefully.
    

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  Aim and Objectives

  Aim and Objectives

  The aim of this virtual training workshop is to provide participants with a comprehensive understanding of Nanopore sequencing technology, from its underlying principles to its practical applications in epidemiological surveillance of infectious diseases. The webinar will enable participants to explore the latest advancements in Nanopore technology, develop key bioinformatics skills for analysing Nanopore sequencing data, and understand its diverse applications in fields such as virology and bacteriology. In this virtual training, a focus will be given on applications to the surveillance and outbreak investigation of pathogens.

  Upon completing this workshop, participants will be able to:

  • Understand the basic principles of Nanopore sequencing

  • Discuss the latest advancements in Nanopore technology

  • Perform bioinformatics analyses using Nanopore data

  • Apply Nanopore sequencing in various areas

  • Recognize the strengths and limitations of Nanopore sequencing
• Pre-requisites
  This topic

  Pre-requisites

  The minimal prerequisites for participants to meet the learning objectives of the practical exercise are:

  • • Ability to navigate a Unix terminal and use bioinformatic command line tools.
  • • Access to a Unix terminal (or emulator) during practical exercises.
  • Participants not having these skills can still attend the virtual training as observers.

    If you are unsure about your command line skills, or if you wish to get some reminders about Unix command line, we encourage you to watch the recordings of the following virtual trainings:

  • • GenEpi-BioTrain - Virtual training 02: From sequencer to polished reads for bacteria
  • • GenEpi-BioTrain - Virtual training 09 & 10 - Unix for beginners & Introduction to the Conda ecosystem
• Software Requirements

  Software Requirements

  For the partial exercise, you need to Install the following software:

  • • Flye (link to download)
  • • BUSCO (link to download)
  • • quast (link to download)
  • • Nanoplot (link to download)
  • How to install?

    The best way to install the software is to use conda environments.
    
    In the same environment you can install Flye, quast and Nanoplot:
    conda create -n flyeconda activate flye
    conda install flye
    conda install bioconda::quast
    conda install -c bioconda nanoplot
    
    For BUSCO, create a different environment, because we have dependencies conflict:
    conda create -n busco
    conda activate busco
    conda install -c conda-forge -c bioconda busco=5.8.2

  • Using Windows? Click here!

    Windows users need to install and run a Unix emulator in windows (e.g., MobaXterm)

• Delivery

  Delivery
  Format

  This virtual training takes place over two sessions that will be held on Wednesday, April 9 and Friday, April 11 from 9:30 to 12:00 (CET).

  
  

  Outline

  Session 1: Introduction to Nanopore: Principles, Updates, and Bioinformatics

  Part 1: Introduction to Nanopore Technology

  Part 2: Assembling Nanopore Data — Practical Exercises

  
  

  The practical exercises presented in Session 1 should be completed between Session 1 and Session 2. The answers will be provided at the beginning of Session 2.

  An announcement will be made once the datasets and materials for the exercise are available.

  
  

  Session 2: Applications to Virology and Bacteriology

  Part 1: Correction of the Practical Exercises

  Part 2: Outbreak tracking of respiratory virus in the field (example of the Avian flu)

  Part 3: State-of-the-Art – Literature on ONT Sequencing Applied to Food Safety.

  • FileAgenda

    
    

• Session 1: Introduction to Nanopore: Principles, Updates, and Bioinformatics

  Session 1: Introduction to Nanopore: Principles, Updates, and Bioinformatics

  1. Introduction to Nanopore Technology (60 min)

  Speaker: Dr. Chloé Baum (Biomics Platform, Institut Pasteur, France)

  — Brief introduction to sequencing

  — Overview of the Biomics platform

  — The basics of Nanopore sequencing 

  — Applications of Nanopore sequencing

  — Challenges and future directions

  — Q&A

  2. Assembling Nanopore data — Practical Exercises (60 min)

  Speaker:  Rania Ouazahrou (Biomics Platform, Institut Pasteur, France)

  — Quality control of FASTQ files 

  — Introduction to genome assembly with Nanopore data

  — Introduction of tools to process and analyse Nanopore data

  — Q&A

  • S1 - Select the checkbox to the right once you have completed watching the recorded session
    

  • Lecture

  • FileIntroduction to Nanopore technology
  • Practical

    Here you can find the practical exercises that should be completed before Session 2. Answers will be given at the beginning of Session 2.
    

  • FileGenome assembly using Nanopore data
  • FolderDatasets
• Session 2: Applications to Virology and Bacteriology

  Session 2: Applications to Virology and Bacteriology

  1. Correction of the Assembly (30min)

  Speaker:  Rania Ouazahrou (Biomics Platform, Institut Pasteur, France)

  — Assembly results and quality control of FASTA files

  — Q&A

  2.  Outbreak tracking of respiratory virus in the field (example of the Avian flu) (40 min)

  Speaker: Dr. Guillaume Croville (National Veterinary School Toulouse, France)

  — How Nanopore technology is used for the outbreak tacking and pathotyping of respiratory viruses in the field (e.g: Influenza virus) 
  — Nanopore sequencing for metagenomic studies

  — Q&A

  3. State-of-the-art – Literature on ONT Sequencing Applied to Food Safety. (30 min)

  Speaker: Ms. Niamh Lacy-Roberts (Technical University of Denmark, Denmark)

  • S2 - Select the checkbox to the right once you have completed watching the recorded session
    

  • Lectures

  • FileOutbreak tracking of respiratory virus in the field (example of the Avian flu)
  • FileState-of-the-art – literature on ONT sequencing applied to food safety, microbiology research and public health surveillance.
  • Practical Exercise

  • FileCorrection of the Assembly
• Contacts

  Contacts

  For any questions regarding the this webinar series, please use the discussion forum.

  If you have questions regarding other training initiatives please contact: courses@ecdc.europa.eu.

  If you have technical issues please contact ECDC Helpdesk - ICT Front Office ICT.FrontOffice@ecdc.europa.eu.