APPLICATION CLOSED - PARTICIPANTS HAS BEEN SELECTED

Training course: Intro to Bioinformatics for genomic data mining

Draft agenda 

Three foodborne pathogens in the joint EFSA-ECDC database. The first three editions focused on the analysis of Pulsed Field Gel Electrophoresis profiles, the molecular data accepted at that time in the database. However, a transition to WGS data for implementation in this database is foreseen for the near future, and it was agreed that, starting from the last edition held at EURL Listeria monocytogenes in 2019, the joint courses should be focused on the analysis of NGS data. Unfortunately, due to the Covid-19 pandemic, no joint trainings could be organised in 2020 and 2021. Following a discussion in the Inter EURLs WG on NGS, it was decided that the 2022 edition will be jointly organised by all the EURLs part of the WG, namely: EURL VTEC, EURL Listeria monocytogenes, EURL Salmonella, EURL Coagulase Positive Staphylococci, EURL Parasites, EURL Foodborne viruses, EURL AMR, EURL Campylobacter.

The training course is held at the Istituto Superiore di Sanità (EURL E. coli) in Rome, Italy, on June 14th-15th 2022. The course starts on June 14th at 9h30 and finishes on June 15th at 14h30. The training course focus on the main features and the use of bioinformatics for analysis of WGS data at a basic level:

❶  Introduction to Next Generation Sequencing (NGS) data formats,
❷ Analysis of NGS data: local and remote options, closed and custom platforms (Galaxy, Ridom Seqsphere+, etc.),
❸ Basic tools for analysis: quality check and trimming,
❹ Assembly, basic typing of the strains using different approaches.

An overview of the possibilities will be given to the participants through hands-on demonstrations and exercises on dry lab analysis. At the end of the course, the participants are expected to be able to use basic bioinformatics tools for analysis of NGS data.

Please note that the participants are asked to bring their own laptops.

The EURLs selection of the participants is based on the following criteria:

► Training needs of the NRL doing the request (may also be based on performance in PTs),
► Participation in previous training initiatives on the same topics,
► Role of the applicant in the NRL,
► Appropriate basic skills of the applicant for a fruitful course,
► If a given laboratory has several NRL mandates, only one applicant from the same laboratory can participate.

EURL reimbursement according to the usual EU Regulations of the selected applicants.