The fourth 'Joint Training Course of the inter EURLs Working Group on NGS: Introduction to Bioinformatics for genomic data mining' was held at ANSES (EURL-CPS and EURL-Listeria monocytogenes) in Maisons-Alfort, France, on 17 and 18 June 2025. 

The latest (and previous) versions of the training presentations are available at the Inter Biorisks-EURLs WG on NGS page on Zenodo via the following links:
1.    Introduction of the inter EURLs Working Group on NGS and the guidance documents released (EURL-VTEC)
2.    Sequencing platforms & output data (EURL-Listeria monocytogenes)
3.    Verification of the integrity of the raw data files (like md5sum) (EURL-Salmonella)
4.    Bioinformatics analysis of NGS data: approaches and opportunities (command-line tools, commercial software, webservers) (EURL-Viruses)
5.    Introduction on quality check and trimming (EURL-VTEC)
6.    Intro ARIES and FastQC and Positional and Quality Trimming on ARIES (EURL-VTEC)
7.    Demo: Quality check and trimming with alternative tools (EURL-Campylobacter)
8.    Introduction on assembly and assembly statistics (EURL-AMR)
9.    Hands-on SPAdes and Quast from ARIES (EURL-VTEC)
10.    Data alignment (EURL-Parasites)
11.    Hands-on E. coli virulotyping using a mapping approach (EURL-VTEC)
12.    Demo: Mapping with Seqsphere (EURL-Listeria monocytogenes)
13.    Amplicon-based sequencing of viral genomes (ISS and EURL-Foodborne Viruses)
14.    Introduction to gene detection using BLAST approach (EURL-CPS)
15.    Hands-on ResFinder on CGE webserver (EURL-AMR)
16.    Introduction to genome comparisons: gene-by-gene vs SNP approach (EURL-Campylobacter)
17.    Demonstration of gene-by-gene approach through different platforms: ARIES (EURL-VTEC), Starflow (EURL-Listeria monocytogenes and EURL-CPS) & Seqsphere (EURL-Salmonella)
18.    Demonstration via Grapetree (EURL-Listeria monocytogenes)
19.    Parasites WGS: opportunities and challenges (EURL-Parasites)
20.    EFSA One Health WGS database and demo (EFSA)

 

The third 'Joint Training Course of the inter EURLs Working Group on NGS: Introduction to Bioinformatics for genomic data mining' was held in Uppsala, Sweden, both at the Swedish Veterinary Agency  (EURL-Campylobacter) on 25 June 2024 and at the Swedish Food Agency (EURL-Foodborne Viruses) on 26 June 2024. Documents, located at the Inter Biorisks-EURLs WG on NGS page on Zenodo, are available through the following link: link to the documents of the third joint training course NGS

 

The second 'Joint Training Course of the inter EURLs Working Group on NGS: Introduction to Bioinformatics for genomic data mining' took place at the location of the EURL-Salmonella in Bilthoven, The Netherlands, on 20 and 21 June 2023.

The program and the presentations can be found below:

 

The first 'Joint Training Course of the inter EURLs Working Group on NGS: Introduction to Bioinformatics for genomic data mining' was held at ISS (EURL-VTEC) in Rome on June 14th - 15th 2022. Documents are available on the EURL-VTEC website: link to the website