Neisseria gonorrhoeae curated genomic dataset used for cg/wgMLST schema creation

Compiled genomic dataset aiming to capture the current known genomic diversity within the circulating populations of Neisseria gonorrhoeae. This dataset included all Illumina-based raw read data from the European Nucleotide Archive (N = 42971), the complete genomes from Genbank (N = 166) and all genomes sequenced at the Portuguese National Institute of Health (N = 2392), up to the 30th of April 2024. All WGS raw read data quality control, contamination assessment, assembly and refinement were performed using the INNUca v4.2.2 pipeline (described in detail at https://github.com/B-UMMI/INNUca). Per sample minimum metadata (i.e., country of origin and collection date) and comprehensive summary reports on genome statistics in every step of the pipeline are provided in this repository.