Panacus: fast and exact pangenome growth and core size estimation

Area of Science:

• Genomics
• Bioinformatics

Background:

• Single linear reference genomes limit the exploration of species' full genomic diversity.
• Pangenomics, representing genomes as graphs, is crucial for overcoming these limitations.
• Scalable software is needed for pangenome analysis, including core genome and pangenome growth quantification.

Purpose of the Study:

• Introduce Panacus (pangenome-abacus), a novel software tool for efficient pangenome graph analysis.
• Enable rapid quantification of universally shared sequences (core genome) and genomic variability (pangenome growth).
• Provide interactive visualization of pangenome analysis results.

Main Methods:

• Panacus processes General Feature Format version 3 (GFA) files, the standard for pangenome graphs.
• The tool is implemented in Rust for high performance.
• Analysis of a human pangenome graph with 110 million nodes is completed in under one hour.

Main Results:

• Panacus enables rapid analysis of large-scale pangenome graphs.
• The software effectively quantifies core genome content and pangenome growth.
• Interactive plots visualize key pangenomic metrics.

Conclusions:

• Panacus addresses the need for scalable pangenome analysis software.
• The tool facilitates deeper exploration of genomic diversity.
• Panacus is available as open-source software with comprehensive documentation.