Rapid-PFP: Accelerating Prefix-Free Parsing with GPU Parallelism (opens in new tab)

Prefix-Free Parsing (PFP) is widely used in genomic data processing to construct compressed indexes on massive, highly repetitive datasets. However, existing CPU implementations are constrained by sequential bottlenecks, limiting their ability to scale to large-scale modern pangenomic collections. We introduce RAPID-PFP, a redesigned implementation of the PFP algorithm that takes advantage of the massive parallelism and high memory bandwidth of modern GPUs. RAPID-PFP parallelizes trigger-stri...