Panacus

Panacus rapidly computes counting statistics for pangenome graph files and visualizes pangenome growth and core genome size.

Key Features:

• Pangenome growth estimation: Measures the extent of genomic variability as a function of sample size.
• Core genome size estimation: Quantifies universally shared sequence across genomes in a pangenome graph.
• GFA file processing: Processes GFA files, the accepted standard for pangenome graph representation.
• Interactive visualization: Generates interactive plots of computed pangenome statistics.
• Scalable performance: Analyzes a human pangenome graph with 110 million nodes in less than one hour.

Scientific Applications:

• Human pangenome analysis: Enables analysis of draft human pangenome graphs to explore full genomic diversity of a species.
• Core genome identification: Identifies universally shared sequences across multiple genomes represented in pangenome graphs.
• Pangenome diversity quantification: Quantifies genomic variability and shared sequence content across increasing numbers of samples.

Methodology:

Panacus is implemented in Rust and computes exact counting statistics on pangenome graphs represented in GFA format.