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Each set represents a different approach to homology-, orthology-, and synteny-based gene clustering as implemented by 6 popular tools for comparative genomics and pangenome analysis (Roary, panX, OrthoFinder, MMseqs2/PanACoTa, CD-HIT, and eggNOG-mapper).  For Escherichia coli, Cutibacterium acnes, Bacteroides uniformis, and Staphylococcus epidermidis, we provide additional sets that combine high-quality genomes with different proportions of medium- and low-quality metagenome-assembled genomes (MAGs).  This dataset is a helpful resource for benchmarking gene clustering tools and pangenome analysis workflows, as well as for testing their robustness with respect to the presence of incomplete or contaminated genomic assemblies.  Reference: Manzano-Morales S, Liu Y, Gonzlez-Bod S, Huerta-Cepas J, Iranzo J. 2022. 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