Panscape: Pangenomics for Bacterial Long Reads

Panscape is presented as an integrated Rust-based command-line framework for processing and summarizing multiple pangenomic data types. Its functionality includes read and FASTQ preprocessing, motif and regular-expression scanning, alignment and annotation support, PAF- and GFA-based graph analysis, VCF comparison, and pangenome database construction. Benchmarking of an optimized implementation on a single-core system showed improved performance in 17 of 18 tested command–dataset combinations, with speedups ranging from 1.05-fold to 2.32-fold. These results suggest that workflow integration and implementation-level optimization can improve the accessibility and efficiency of pangenomic analyses.