In the framework of the activities of the Inter EURLs Working Group on Next Generation Sequencing, the need for guidelines for checking the quality of extracted DNA to be used for sequencing was highlighted. This document is meant to provide guidance in this crucial preliminary step of the laboratory work to produce NGS data.It was agreed to start considering the three pathogens Listeria monocytogenes, Salmonella and Shiga toxin-producing E. coli (STEC), on which the Joint EFSA-ECDC molecular typing data collection is currently focused, with the aim of expanding the topic to other pathogens in a second step.