You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 04 held in November 2023, and certificates are only issued to participants who attended the live webinar sessions.
Welcome to this virtual training space on EVA.
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 aim of this virtual training is to introduce public health participants to theoretical and practical aspects of analysing avian influenza sequence data from single samples in a one health approach. Participants will get insights on NGS data analysis (including data quality control) and genotyping, and their use in the context of avian influenza outbreak investigations.
Upon completion of this workshop, participants will be able to:
This virtual training takes place over two sessions that will be held on 20 and 24 November 2023, 10:00-13:30.
Participants will be assigned a short exercise, which will require 1-3 hours of work, to conduct in between the two online sessions.
Session 1: Introduction to influenza sequences data analysis (mapping/assembly) including quality control and genotyping in the context of avian influenza in Europe. Hands-on exercise (avian influenza case).
Session 2: Discussion of exercise results. Lecture on NGS based outbreak investigation.
For the general lectures there are no prerequisites.
The minimal prerequisites for participants to meet the learning objectives of the NGS data part of the workshop are:
- Ability to navigate a Unix/MacOS terminal and use of bioinformatic command line tools.
- Have access to a terminal.
- Have conda or miniconda installed.
- Read IRMA pipeline publication. (https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3030-6 )
Prior to the training, participants that would like to meet the minimum requirement for the NGS data analysis lecture are expected to download, install, and briefly test conda or miniconda installed.
If on a Unix based OS (Not windows), consider installing miniconda following the official instructions: https://conda.io/projects/conda/en/latest/user-guide/install/index.html
Aim for creating individual environments for each tool separately while installing them, as some tools may have conflicting software dependencies.
This session will include:
Useful links:
UGENE download: https://ugene.net
UGENE tutorial: http://ugene.net/multiple-sequence-alignment-overview/
S1 - Select the checkbox to the right once you have completed watching the recorded session
In this exercise, you will detect avian influenza from mammalian samples and you will need to determine their consensus sequences but also their mutations along the sequences. On top of that, you will use the tools discovered during this course to subtype/genotype the data and potentially (if you have time!) build a phylogeny.
Part 1: Use the tools learned in Session 1 to determine mutations and subtype/genotype the avian sequences.
Part 2: Using IRMA to reconstruct a full influenza genome.
Please have a look at the pdf file "Practical_Avian_Influenza" present in this folder (not in the Data folder) to go through the exercise.
You will be able to answer the questions as soon as the announcement is out.
S2 - Select the checkbox to the right once you have completed watching the recorded session
For any questions regarding the this virtual training, please use the discussion forum.
If you have questions about the GenEpi-BioTrain programme, please address ECDC.Microbiology@ecdc.europa.eu.
If you have questions regarding other training initiatives please contact: Courses@ecdc.europa.eu.
If you have technical issues please contact the ECDC Service Desk at servicedesk@ecdc.europa.eu.
