PanGBank is a web-based platform for exploring, analyzing, and downloading pangenomes generated with PPanGGOLiN. It builds pangenomes using a Nextflow workflow (labgem/PanGBank-wf) and provides access through a public REST API .
Pangenomes are organized into collections based on genome source and taxonomy, providing a structured and scalable framework for comparative genomics. The web application allows users to search pangenomes by taxonomy, genome, or strain; visualize statistics; browse annotations with CGView genome maps; navigate between genomes; and download the corresponding PPanGGOLiN files.
A companion command-line tool (labgem/PanGBank-cli) provides easy access to the API for querying and downloading pangenome data directly from the terminal. Use case examples are available in our labgem/PanGBank-tutorial repository.
PPanGGOLiN (Gautreau et al., 2020) is a software suite for constructing and analyzing prokaryotic pangenomes. It uses a statistical model instead of fixed thresholds to partition the pangenome. This approach enables robust analysis of low-quality data such as MAGs and SAGs, making it suitable for large-scale environmental studies and uncultivable species.
PPanGGOLiN builds a Partitioned Pangenome Graph by integrating gene content and genomic neighborhood information. Gene families form nodes, and edges represent genetic contiguity. The statistical model partitions gene families into persistent, shell, and cloud genomes, with neighboring families more likely to belong to the same partition.
The panRGP method (Bazin et al., 2020) identifies Regions of Genome Plasticity (RGPs), which are clusters of shell and cloud genes often acquired through horizontal gene transfer and corresponding to Genomic Islands. RGPs are grouped into spots of insertion based on shared flanking persistent genes. These regions can be further divided into conserved modules using panModule (Bazin et al., 2021), which identifies co-occurring, co-localized genes that are gained or lost together in the variable regions of the pangenome.
PanGBank is mainly developed by the LABGeM team at Genoscope:
Jean Mainguy
David Vallenet
Alexandra Calteau
Téo Lemane
Thanks to the prior contribution of Adelme Bazin and Guillaume Gautreau.
PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN
Mainguy J, Lemane T, Bazin A, Arnoux J, Gautreau G, Médigue C, Calteau A, Vallenet D. (2026)
Nucleic Acids Research.
doi:10.1093/nar/gkag948
PanGBank pangenomes are constructed with PPanGGOLiN and its companion tools. If your research makes use of these underlying methods, please also cite the relevant references:
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
Gautreau G et al. (2020)
PLOS Computational Biology, 16(3): e1007732.
doi:10.1371/journal.pcbi.1007732
panRGP: a pangenome-based method to predict genomic islands and explore their diversity
Bazin A et al. (2020)
Bioinformatics, 36(Supplement_2): i651–i658.
doi:10.1093/bioinformatics/btaa792
panModule: detecting conserved modules in the variable regions of a pangenome graph
Bazin A et al. (2021)
bioRxiv.
doi:10.1101/2021.12.06.471380
Our pangenome data and associated resources are made freely available under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) License.
This license allows you to:
As long as you give appropriate credit, provide a link to the license, indicate if changes were made, and distribute adaptations under the same license.
Our GTDB-based pangenome collections use and adapt taxonomy from the Genome Taxonomy Database (GTDB), which is distributed under CC BY-SA 4.0. PanGBank integrates this taxonomy into its pangenome collections and associated metadata. GTDB is not affiliated with, and does not endorse, PanGBank.
For full license details, please see the official CC BY-SA 4.0 page.
PanGBank builds upon several community-developed resources.
Genome Taxonomy Database (GTDB). The current PanGBank collections (GTDB_all and GTDB_refseq) are organized using the taxonomy provided by the GTDB (Parks et al., 2025).
CGView.js and ProkSee. PanGBank uses CGView.js (Grant et al., 2026) to generate the interactive circular genome maps displayed throughout the website. These maps can be exported directly to proksee.ca (Grant et al., 2023) for further exploration and customization.
This work was financially supported by:
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If you have any questions, please open an issue on our GitHub repository at https://github.com/labgem/PanGBank-api or contact us at labgem@genoscope.cns.fr.