TY - JOUR
T1 - quickLD
T2 - An efficient software for linkage disequilibrium analyses
AU - Theodoris, Charalampos
AU - Low, Tze Meng
AU - Pavlidis, Pavlos
AU - Alachiotis, Nikolaos
N1 - Funding Information:
We would like to thank the anonymous reviewers and the editor for their comments that helped us to improve the clarity of this manuscript.
Publisher Copyright:
© 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
PY - 2021/10
Y1 - 2021/10
N2 - 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.
AB - 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.
KW - UT-Hybrid-D
U2 - 10.1111/1755-0998.13438
DO - 10.1111/1755-0998.13438
M3 - Article
SN - 1755-098X
VL - 21
SP - 2580
EP - 2587
JO - Molecular Ecology Resources
JF - Molecular Ecology Resources
IS - 7
ER -