PanGeneWhale - A dockerized Kotlin-based GUI platform for reproducible and user-friendly pangenomic analysis
Walter de Barros Gomes Netto1, Saed Silva Sousa2, Sofia Mayumi Brandao Nakamaru3
1Biological Engineering Laboratory, Guamá Science and Technology Park, Belém, Pará, Brazil.
Computational Biology and Chemistry
|November 21, 2025
Summary
PanGeneWhale simplifies pangenomic analysis by integrating multiple tools into a user-friendly platform. This computational tool enhances accessibility and reproducibility for researchers studying microbial genomes.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Pangenomic analysis tools face challenges in usability, performance, and complexity.
- These barriers limit accessibility and reproducibility, requiring advanced computational expertise.
Purpose of the Study:
- To develop PanGeneWhale, a unified computational platform simplifying pangenomic analysis.
- To enhance accessibility, reproducibility, and efficiency in large-scale genomic studies.
Main Methods:
- Integration of multiple pangenomic analysis tools within a Docker container environment.
- Development of an intuitive, cross-platform graphical user interface.
- Validation using 50 Escherichia coli genomes and benchmarking of computational performance.
Main Results:
- PanGeneWhale successfully integrates diverse tools, automating execution flows and ensuring reproducible results.
- Benchmarking revealed performance disparities among tools, which PanGeneWhale addresses.
- Identified and resolved critical usability issues like outdated dependencies and lack of GUIs.
Conclusions:
- PanGeneWhale significantly improves the accessibility and efficiency of pangenomic analysis for researchers of all skill levels.
- The platform enhances the practicality and reliability of large-scale genomic studies.
- PanGeneWhale overcomes previous limitations, making advanced pangenomic analyses more manageable.
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