Next Generation Sequencing

This page provides information and documents generated by the Inter-European Union Reference Laboratories Working Group on Next Generation Sequencing.

The Inter-European Union Reference Laboratories (EURLs) Working Group (WG) has been established by the European Commission with the aim to promote the use of Next Generation Sequencing (NGS) across the EURLs' networks, build NGS capacity within the EU and ensure liaison with the work of the EURLs and the work of EFSA and ECDC on the NGS mandate sent by the Commission. The WG includes all the EURLs operating in the field of the microbiological contamination of food and feed and is coordinated by the EURL for E. coli.

Membership of the Inter EURL WG on NGS:

EURL-E. coli (coordinator)
EURL-Listeria monocytogenes
EURL-Coagulase Positive Staphylococci
EURL-Salmonella
EURL-Campylobacter
EURL-Parasites
EURL-Antimicrobial Resistance
EURL-Food borne viruses
Observers: SANTE G4, EFSA, ECDC

The documents are meant to provide guidance to the laboratories in the area of application of NGS and have been produced by the WG with the aim of being diffused to all the networks of NRLs. These documents are aggregated in the Zenodo community Inter Biorisks-EURLs WG on NGS.

Deliverable	Document	Curated by
1	Overview of conducted and planned PTs	EURL-Antimicrobial Resistance
2	Reference WGS collection	EURL-Salmonella
3	Guidance document for WGS-laboratory procedures	EURL-Parasites
4	Bioinformatics tools for basic analysis of Next Generation Sequencing data	EURL-E. coli
5	Guidance document for cluster analysis of whole genome sequence data	EURL-Campylobacter
6	Guidance document for NGS-Benchmarking	EURL-Listeria monocytogenes
7	Inventory of training supports	EURL-Coagulase Positive Staphylococci
8	Survey on the use of NGS across the NRLs networks	EURL-E. coli
9	Supporting document for preparing high quality DNA for Whole Genome Sequencing	EURL-E. coli
10	Guidelines for Dry-Lab Quality Control Metrics and Acceptance Thresholds in Short-Read WGS of zoonotic and indicator bacteria	EURL-Listeria monocytogenes
11	Guidelines for amplicon sequencing of the capsid region of noroviruses	EURL-Food borne virues
12	Guidelines for the validation of Whole Genome Sequencing for accreditation	EURL-E. coli

Last reviewed 26/01/2026