Multi-method gene clusters at species-level resolution for 125 prokaryotic pangenomes

This dataset contains 9 sets of species-level gene clusters and high-resolution species trees for 125 representative bacterial and archaeal species, encompassing a total of 6,851 nearly complete genomes. 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. References: Manzano-Morales S, Liu Y, González-Bodí S, Huerta-Cepas J, Iranzo J. 2023. Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses. Genome Biol 24, 250, doi: 10.1186/s13059-023-03089-3