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

<p>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).</p> <p>For <em>Escherichia coli</em>, <em>Cutibacterium acnes</em>, <em>Bacteroides uniformis</em>, and <em>Staphylococcus epidermidis</em>, we provide additional sets that combine high-quality genomes with different proportions of medium- and low-quality metagenome-assembled genomes (MAGs).</p> <p>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.</p> <p><strong>Reference:</strong> Manzano-Morales S, Liu Y, Gonz&aacute;lez-Bod&iacute; S, Huerta-Cepas J, Iranzo J. 2022. Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses. <em>bioRxiv</em> doi: <a href="https://doi.org/10.1101/2022.09.25.509376">10.1101/2022.09.25.509376</a></p>