Coordinated Meta-Storms enables comparison of million-level microbiomes

Motivation Phylogeny-based distance serves as the foundation in the evaluation of microbiome beta diversity. However, the exponential growth of data volume has recently introduced substantial computational challenges, while current methods remain limited in their scalability and efficiency. Results : To solve these issues, we introduce Coordinated Meta-Storms (CMS), a novel approach for large-scale microbiome phylogeny-based distance calculation. CMS incorporates a dynamic multiple GPU (Graphics Processing Unit) architecture based on a self-adaptive data decomposition strategy and optimization, which empowers pairwise comparison of million-level microbiomes within 40 hours on a single computing node. Availability and implementation Coordinated Meta-Storms is implemented by CUDA, HIP and C ++. Source code is available at GitHub (https://github.com/qdu-bioinfo/Coordinated-Meta-Storms) and has been published on Zenodo (DOI: 10.5281/zenodo.15802999). Supplementary information Supplementary data are available at Bioinformatics online.