Validation of WGS pipeline for analysis of Neisseria meningitidis isolates

We developed an optimized user-friendly pipeline for the routine analysis of Neisseria meningitidis isolates to provide an alternative based on WGS compared to conventionally employed molecular typing methods. The pipeline uses Illumina data to perform automated data processing and quality control, and provides results for three assays: antibiotic resistance gene detection, sequence typing and serogroup determination. A collection of 67 reference strains was sequenced to extensively validate the performance of the pipeline, for which we proposed a strategy.