Webpage of the inter EURLs Biorisks working group on NGS

TUESDAY 25 JUNE 2024

09.15 Introduction of the inter EURLs Working Group on NGS and the guidance documents released (EURL-VTEC)

09.30 Introduction to WGS

1. Sequencing platforms & output data (20’) (EURL-Listeria monocytogenes)
2. Verification of the integrity of the raw data files (like md5sum) (EURL-Salmonella)
3. Bioinformatics analysis of NGS data: approaches and opportunities (command-line tools, commercial software, webservers) (EURL-Viruses)

10.50 Introduction on quality check and trimming (EURL-VTEC)

11.10 Hands-on exercises – Quality check and trimming

Quality check and trimming using different tools and platforms. Results interpretation.

• Intro ARIES and FastQC and Positional and Quality Trimming on ARIES (EURL-VTEC)
• Demo: Quality check and trimming with alternative tools (EURL-Campylobacter)

13.40 Introduction on assembly and assembly statistics (EURL-AMR)

14.00 Hands-on exercises – Assembly statistics

Assembly statistics using different tools and platforms. Results interpretation.

• Hands-on SPAdes and Quast from ARIES (EURL-VTEC)

15.00 Data alignment (EURL-Parasites)

15.20 Hands-on exercises – Mapping approach

Demonstration of mapping through different platforms.

• Hands-on E. coli virulotyping using a mapping approach (EURL-VTEC)
• Demo: Mapping with Seqsphere (EURL-Listeria monocytogenes)

16.20 Amplicon-based sequencing of viral genomes (ISS and EURL-Foodborne Viruses)

WEDNESDAY 26 JUNE 2024

9.00 Introduction to gene detection using BLAST approach (EURL-CPS)

9.15 Hands-on exercises – Search of genetic features on contigs

Identification of virulence and AMR genes using different tools and platforms. Results interpretation.
Demonstration of genes identification on contigs through different platforms.

• Hands-on ResFinder on CGE webserver (EURL-AMR)
• Demo: Salmonella virulotyping with Seqsphere (EURL-Salmonella)

10.10 Introduction to genome comparisons: gene-by-gene vs SNP approach (EURL-Campylobacter)

11.00 Demonstration of gene-by-gene approach through different platforms:

• ARIES (EURL-VTEC)
• Starflow (EURL-Listeria monocytogenes and EURL-CPS)
• Seqsphere (EURL-Salmonella)

11.45 Parasites WGS: opportunities and challenges (EURL-Parasites)

13.15 Hands-on exercises – Visualisation of clustering data

Demonstration via Grapetree (EURL-Listeria monocytogenes)

13.45 EFSA One Health WGS database and demo (EFSA)

Locations:

• Swedish Veterinary Agency (SVA) - Ulls väg 2B - Uppsala
• Swedish Food Agency (SFA) - Dag Hammarskölds väg 56A - Uppsala

Organised by:

• EURL-AMR
• EURL-Campylobacter
• EURL-Coagulase Positive Staphylococci (CPS)
• EURL-Foodborne viruses
• EURL-Listeria monocytogenes
• EURL-Parasites
• EURL-Salmonella
• EURL-VTEC