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Panalyze: automated virus pangenome variation graph construction, analysis and annotation
Chandana Tennakoon1, Thibaut Freville1, Tim Downing1
1Pirbright Institute, Surrey, GU24 0NF, UK.
Bioinformatics Advances
|March 23, 2026
Summary
We developed Panalyze, a tool for creating and analyzing viral pangenome variation graphs (PVGs). This pipeline offers scalable, laptop-friendly analysis of viral genomic diversity, overcoming limitations of existing methods.
Area of Science:
- Bioinformatics
- Computational Biology
- Virology
Background:
- Pangenome variation graphs (PVGs) offer insights into viral genomic diversity by reducing reference bias.
- Existing methods for PVG analysis are computationally intensive and do not scale well for smaller viral genomes.
- Automating PVG construction and analysis is essential for exploratory investigations and optimization.
Purpose of the Study:
- To develop a computationally scalable and easily deployable pipeline for virus PVG construction and analysis.
- To address the limitations of existing methods in handling smaller viral genomes and laptop environments.
- To facilitate rapid creation and analysis of virus PVGs with a broad range of applications.
Main Methods:
- Developed Panalyze, a tool implemented in NextFlow and containerized in Docker for virus PVG construction, analysis, and annotation.
- Utilized NextFlow for efficient task completion across multiple compute nodes and diverse environments.
- Ensured Panalyze can operate on a single thread on a standard laptop, analyzing sequences of any length.
Main Results:
- Panalyze provides a computationally scalable solution for virus PVG construction and analysis.
- The tool is adaptable to various computing environments, including single-laptop analysis.
- Demonstrated the utility of Panalyze using common viral pathogens, showcasing valuable outputs.
Conclusions:
- Panalyze facilitates the rapid creation and analysis of virus PVGs, enhancing the study of viral genomic diversity.
- The pipeline overcomes scalability and accessibility limitations of previous methods.
- Panalyze is available as an open-source tool, promoting wider adoption in viral research.
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