Straightforward and reproducible analysis of bacterial pangenomes using Pagoo

Pangenome analysis is fundamental to explore evolutionary processes occurring in bacterial populations. However, the lack of standardized methods for handling diverse pangenomic datasets and complex metadata hinders more straightforward and reproducible downstream analyses. To fill this gap, we introduce Pagoo, a new framework that integrates pangenome data, analytical methods and visualization tools in a single object that can be easily stored, shared and responsively queried for improved biological interpretation of bacterial evolution.