This document specifies the minimum requirements for generating and analysing whole genome sequencing (WGS) data of bacteria obtained from the food chain. This process can include the following stages:

a) handling of bacterial cultures;

b) axenic genomic DNA isolation;

c) library preparation, sequencing, and assessment of raw DNA sequence read quality and storage;

d) bioinformatics analysis for determining genetic relatedness, genetic content and predicting phenotype, and bioinformatics pipeline validation;

e) metadata capture and sequence repository deposition;

f) validation of the end-to-end WGS workflow (fit for purpose for intended application).

This document is applicable to bacteria isolated from:

—    products intended for human consumption;

—    products intended for animal feed;

—    environmental samples from food and feed handling and production areas;

—    samples from the primary production stage.