quickLD: An efficient software for linkage disequilibrium analyses

Charalampos Theodoris, Tze Meng Low, Pavlos Pavlidis, Nikolaos Alachiotis*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

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.
Original languageEnglish
Number of pages8
JournalMolecular Ecology Resources
Early online date10 Jun 2021
DOIs
Publication statusPublished - 2021

Keywords

  • UT-Hybrid-D

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