PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN
Abstract
PanGBank (https://pangbank.genoscope.cns.fr) is a comprehensive open-access database providing precomputed prokaryotic pangenomes at a broad taxonomic scale. Built upon PPanGGOLiN partitioned pangenome graphs, PanGBank addresses the growing need for large-scale comparative genomics through a standardized, regularly updated, and fully accessible resource. The initial release comprises two complementary collections covering >4600 prokaryotic species from the Genome Taxonomy Database (GTDB), encompassing over 393 000 genomes: GTDB_all, maximizing taxonomic and environmental diversity through the inclusion of metagenome-assembled genomes and single-cell amplified genomes, and GTDB_refseq, focusing on high-quality, annotation-rich genomes. Each species-level pangenome integrates graph-based statistical partitions into persistent, shell, and cloud gene families, together with regions of genomic plasticity (panRGP) and co-localized functional modules (panModule). PanGBank offers multiple access modes, including a REST API, a command-line interface, and an interactive web interface. By combining large-scale pangenome resources with advanced graph-based analyses, PanGBank provides a scalable framework for exploring microbial diversity, genome evolution, functional variation, and the dissemination of adaptive traits across prokaryotic populations, as illustrated by a use case on Acinetobacter baumannii pangenome investigating the distribution and evolution of antimicrobial resistance determinants.
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BibTeX
@article{mainguy2026pangbank,
title = {{PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN}},
author = {Jean Mainguy and Téo Lemane and Adelme Bazin and Jérôme Arnoux and Guillaume Gautreau and Claudine Médigue and Alexandra Calteau and David Vallenet},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag948},
url = {https://hal.science/hal-05779522v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN
AU - Jean Mainguy
AU - Téo Lemane
AU - Adelme Bazin
AU - Jérôme Arnoux
AU - Guillaume Gautreau
AU - Claudine Médigue
AU - Alexandra Calteau
AU - David Vallenet
PY - 2026
DA - 2026/10/05
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag948
UR - https://hal.science/hal-05779522v1
AB - PanGBank (https://pangbank.genoscope.cns.fr) is a comprehensive open-access database providing precomputed prokaryotic pangenomes at a broad taxonomic scale. Built upon PPanGGOLiN partitioned pangenome graphs, PanGBank addresses the growing need for large-scale comparative genomics through a standardized, regularly updated, and fully accessible resource. The initial release comprises two complementary collections covering >4600 prokaryotic species from the Genome Taxonomy Database (GTDB), encompassing over 393 000 genomes: GTDB_all, maximizing taxonomic and environmental diversity through the inclusion of metagenome-assembled genomes and single-cell amplified genomes, and GTDB_refseq, focusing on high-quality, annotation-rich genomes. Each species-level pangenome integrates graph-based statistical partitions into persistent, shell, and cloud gene families, together with regions of genomic plasticity (panRGP) and co-localized functional modules (panModule). PanGBank offers multiple access modes, including a REST API, a command-line interface, and an interactive web interface. By combining large-scale pangenome resources with advanced graph-based analyses, PanGBank provides a scalable framework for exploring microbial diversity, genome evolution, functional variation, and the dissemination of adaptive traits across prokaryotic populations, as illustrated by a use case on Acinetobacter baumannii pangenome investigating the distribution and evolution of antimicrobial resistance determinants.
SN - 0305-1048
SN - 1362-4962
ER -