PanGeneWhale - A dockerized Kotlin-based GUI platform for reproducible and user-friendly pangenomic analysis

The choice of tools for pangenomic analysis represents an ongoing challenge, due to factors such as usability, computational performance, operational complexity and the diversity of solutions available. These barriers often require advanced technical knowledge, which can compromise both the accessibility and reproducibility of the analyses. To overcome these limitations, PanGeneWhale was developed, a computational platform that integrates multiple tools in a unified environment based on Docker containers. Equipped with an intuitive, cross-platform graphical interface, PanGeneWhale automates execution flows, ensures reproducibility of results and expands access to pangenomic analyses in a simplified and efficient manner. In this way, the tool supports both researchers with little computer experience and advanced users, enabling large-scale studies with greater practicality and reliability. In the process of validating PanGeneWhale, 50 Escherichia coli genomes were used to test and evaluate all the integrated tools. In addition, a benchmarking study was conducted, which highlighted disparities in computational performance, including CPU, memory and storage usage, as well as differences in the biological composition of the pangenomes generated. The study also identified critical usability barriers, such as outdated dependencies and the absence of graphical interfaces, which were fully resolved with the development of PanGeneWhale. Available at https://github.com/allanverasce/pangenewhale.