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.