协调元风暴可实现百万级微生物群落的比较。
Coordinated Meta-Storms enables comparison of million-level microbiomes.
作者信息
Wang Minan, Gao Hao, Zhang Yu, Huang Yongxiang, Su Xiaoquan
机构信息
College of Computer Science and Technology, Qingdao University, Qingdao, Shandong 266071, China.
出版信息
Bioinformatics. 2025 Aug 2;41(8). doi: 10.1093/bioinformatics/btaf438.
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 Graphics Processing Unit architecture based on a self-adaptive data decomposition strategy and optimization, which empowers pairwise comparison of million-level microbiomes within 40 h 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).
动机
基于系统发育的距离是评估微生物群落β多样性的基础。然而，近年来数据量的指数增长带来了巨大的计算挑战，而当前方法在可扩展性和效率方面仍然有限。
结果
为了解决这些问题，我们引入了协调元风暴（CMS），这是一种基于大规模微生物群落系统发育距离计算的新方法。CMS采用了基于自适应数据分解策略和优化的动态多图形处理单元架构，能够在单个计算节点上40小时内对百万级微生物群落进行成对比较。
可用性和实现
协调元风暴由CUDA、HIP和C++实现。源代码可在GitHub（https://github.com/qdu-bioinfo/Coordinated-Meta-Storms）上获取，并已在Zenodo上发布（DOI：10.5281/zenodo.15802999）。
Zotero 插件