Multi-method gene clusters at species-level resolution for 125 prokaryotic pangenomes
- 1. Barcelona Supercomputing Centre (BSC-CNS) - Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
- 2. Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain.
- 3. Centro de Biotecnología y Genómica de Plantas (UPM-INIA)
Description
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.
Reference: Manzano-Morales S, Liu Y, González-Bodí S, Huerta-Cepas J, Iranzo J. 2022. Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses. bioRxiv doi: 10.1101/2022.09.25.509376
Notes
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Additional details
Related works
- Is supplement to
- Preprint: 10.1101/2022.09.25.509376 (DOI)