Software tools for linkage disequilibrium (LD) analyses are designed to calculate LD among all genetic variants in a single region. Since compute and memory requirements grow quadratically with the distance between variants, using these tools for long-range LD calculations leads to long execution times and increased allocation of memory resources. Furthermore, widely used tools do not fully utilize the computational resources of modern processors and/or graphics processing cards, limiting future large-scale analyses on thousands of samples. We present quickLD, a stand-alone and open-source software that computes several LD-related statistics, including the commonly used r². quickLD calculates pairwise LD between genetic variants in a single region or in arbitrarily distant regions with negligible memory requirements. Moreover, quickLD achieves up to 95% and 97% of the theoretical peak performance of a CPU and a GPU, respectively, enabling 21.5× faster processing than current state-of-the-art software on a multicore processor and 49.5× faster processing when the aggregate processing power of a multicore CPU and a GPU is harnessed. quickLD can also be used in studies of selection, recombination, genetic drift, inbreeding and gene flow. The software is available at https://github.com/pephco/quickLD.

中文翻译：

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quickLD：一种高效的连锁不平衡分析软件

用于连锁不平衡 (LD) 分析的软件工具旨在计算单个区域中所有遗传变异的 LD。由于计算和内存需求随着变体之间的距离呈二次方增长，因此使用这些工具进行远程 LD 计算会导致执行时间延长并增加内存资源分配。此外，广泛使用的工具没有充分利用现代处理器和/或图形处理卡的计算资源，限制了未来对数千个样本的大规模分析。我们介绍了 quickLD，这是一个独立的开源软件，可以计算几个与 LD 相关的统计数据，包括常用的r ². quickLD 计算单个区域或任意遥远区域的遗传变异之间的成对 LD，内存需求可忽略不计。此外，quickLD 分别实现了 CPU 和 GPU 理论峰值性能的 95% 和 97%，在多核处理器上实现了比当前最先进软件快 21.5 倍的处理速度和 49.5 倍的处理速度。多核 CPU 和 GPU 的综合处理能力得到利用。quickLD 还可用于选择、重组、遗传漂变、近亲繁殖和基因流动的研究。该软件可从 https://github.com/pephco/quickLD 获得。