According to Commission Implementing Regulation (EU) 2025/179 (1), Whole Genome Sequencing (WGS) shall be performed on isolates of food-borne pathogens associated with food-borne outbreaks. For this, National Reference Laboratories and/or Official Laboratories shall be accredited for this method according to EN ISO/IEC 17025:2017 (1). To enable National Accreditation Bodies to assess laboratories in a harmonised way, European Accreditation has published a Guideline for the Accreditation of Laboratories carrying out Genetic Testing using Next Generation Sequencing (NGS) Techniques (EA 4/24- G: 2025) (3).The present document produced by the Inter EURLs WG for NGS does not replace the procedures of the Quality Assurance Systems in use in the accredited laboratories, but it is meant to be used alongside, with the aim of giving reference to internationally recognized rules and procedures acknowledged by standards, where available, or other documents that can be used for the technical validation of the WGS workflow. This document considers all steps of the workflow, including both wet lab and dry lab, but does not comprise the accreditation of the cluster analysis as this guidance document is meant to facilitate the accreditation of WGS workflow to respond to the Commission Implementing Regulation (EU) 2025/179 (produce data and send to EFSA) (1). For additional information and specific requests regarding the different pathogens, the specific EURLs can be contacted at the following addresses: EURL for Campylobacter: eurl-campylobacter@sva.se EURL for Escherichia coli: crl.vtec@iss.it EURL for Listeria monocytogenes: eurl-listeria@anses.fr EURL for Salmonella: EURLSalmonella@rivm.nl