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quickLD: an efficient software for linkage disequilibrium analyses

Theodoris Charalabos, Low Tze Meng, Pavlidis Pavlos, Alachiotis Nikolaos

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URIhttp://purl.tuc.gr/dl/dias/F69E76A9-39D9-43AC-AAE2-BFF2144FB425-
Αναγνωριστικόhttps://doi.org/10.1111/1755-0998.13438-
Αναγνωριστικόhttps://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13438-
Γλώσσαen-
Μέγεθος8 pagesen
ΤίτλοςquickLD: an efficient software for linkage disequilibrium analysesen
ΔημιουργόςTheodoris Charalabosen
ΔημιουργόςΘεοδωρης Χαραλαμποςel
ΔημιουργόςLow Tze Mengen
ΔημιουργόςPavlidis Pavlosen
ΔημιουργόςAlachiotis Nikolaosen
ΕκδότηςWileyen
ΠερίληψηSoftware 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.en
ΤύποςPeer-Reviewed Journal Publicationen
ΤύποςΔημοσίευση σε Περιοδικό με Κριτέςel
Άδεια Χρήσηςhttp://creativecommons.org/licenses/by-nc/4.0/en
Ημερομηνία2022-11-08-
Ημερομηνία Δημοσίευσης2021-
Θεματική ΚατηγορίαComputer programen
Θεματική ΚατηγορίαHigh-performance softwareen
Θεματική ΚατηγορίαLinkage disequilibriumen
Βιβλιογραφική ΑναφοράC. Theodoris, T. M. Low, P. Pavlidis, and N. Alachiotis, “quickLD: an efficient software for linkage disequilibrium analyses,” Mol. Ecol. Resour., vol. 21, no. 7, pp. 2580–2587, Oct. 2021, doi: 10.1111/1755-0998.13438.en

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