This entry contains raw data sets from chewBBACA and Panaroo, used to create and validate a core genome MLST scheme for the Bacillus cereus group of bacteria. 1. Creation of a cgMLST scheme from 173 closed B. cereus group genomes using chewBBACA (file S1). The latest assemblies of 2458 Bacillus cereus group genomes available (October, 2021) were downloaded from the NCBI GenBank FTP site, of which 173 were complete (i.e., ungapped, fully closed chromosome and plasmid sequences) genomes. A cgMLST scheme was defined using the chewBBACA 2.8.5 pipeline on the closed genome set. 2. Core genome from 173 closed Bacillus cereus group genomes using Panaroo (file S2). For comparison we analyzed the core genome using the most recent pan-genome software, Panaroo. 3. Application of the cgMLST scheme (from 1) to 2458 B. cereus group genomes (file S3). The cgMLST scheme created from 173 closed B. cereus group genomes using chewBBACA (1) was applied to the full set of 2458 B. cereus group genomes available. Allelic profiles for the loci in the scheme were determined using the "AlleleCall" operation in chewBBACA.