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This supplemental material includes the genome assemblies, associated metadata and analysis results for five datasets used to define a publicly available annotated wgMLST schema for S. pyogenes and to evaluate its suitability for high resolution typing. A brief description for each file in the dataset is available in the included README file. Raw sequencing data and sample metadata for the 265 isolates included in Dataset1 have been deposited in the European Nucleotide Archive (ENA) under Project PRJEB49967. The wgMLST schema was created with chewBBACA and is publicly available at chewie-NS, where a more detailed description of schema creation, annotation and curation can be found.

RM was supported by Fundação para a Ciência e Tecnologia (grant 2020.08493.BD). Partial support was received from ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI – Fundos Europeus Estruturais e de Investimento from Programa Operacional Regional Lisboa 2020 and by national funds from FCT–Fundação para a Ciência e a Tecnologia, and by the LISBOA-01-0145-FEDER-007391 project, cofunded by FEDER through POR Lisboa 2020 –Programa Operacional Regional de Lisboa, PORTUGAL 2020, and Fundação para a Ciência e a Tecnologia.