You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 03 held in September 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.
Aim
The aim of this virtual training is to introduce participants to theoretical and practical aspects of analysing SARS-CoV-2 amplicon sequence data (mainly ARTIC amplicon panels) from single patient samples. Participants will get insights into the background of amplicon panels, analysis steps and tools, as well as data quality control.
Objectives
After completing this course, you will be able to conduct a basic analysis of SARS-CoV-2 amplicon sequencing data to detect mutations and determine the variant. Participants will have a basic understanding of the analysis steps and quality control parameters.
Out of scope
This virtual training cannot cover all existing amplicon approaches. You will not learn about analysis of pooled samples or wastewater surveillance, evolutionary rates of lineages or dated phylogenetic trees.
This virtual training takes place over two sessions that will be held on 25 and 26 September 2023, from 09:00-12:30. Participants will be assigned some exercises to conduct in between the two online sessions.
Session 1: Introduction to SARS-CoV-2 and amplicon-sequencing. Hands-on Illumina DRAGEN COVID Lineage app.
Session 2: Discussion of exercise results. Basics of data analysis (amplicon/mapping/assembly). Showcase of the SARSCOV2seq bioinformatics pipeline. Tools and pipeline options.
For the exercise, participants will be asked to analyse amplicon sequencing data of SARS-CoV-2 with the DRAGEN COVID Lineage app on the Illumina BaseSpace cloud.
A free Illumina BaseSpace account is required and should be registered before the training. (Create an account here)
Details and instructions for the exercise will be given in Module 1.
After attending this session participants will be able to:
· Describe what is SARS-CoV-2 and
amplicon-sequencing.
· Use the basic functionality of Illumina DRAGEN COVID Lineage app.
S1 - Select the checkbox to the right once you have completed watching the recorded session
After attending this session participants will be able to:
Better use the DRAGEN COVID Lineage app.
Describe the basic steps in the SARS-CoV-2 bioinformatics pipeline
Explain the outputs of the SARSCOV2seq bioinformatics pipeline.
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.
