Scalable linkage-disequilibrium-based selective sweep detection: a performance guide

GigaScience

Table 1 Execution times (in seconds) for the analysis of DNA datasets in different shapes

Sequences	100			1,000			10,000			50,000
Sites	10,000	50,000	100,000	10,000	50,000	100,000	10,000	50,000	100,000	10,000	50,000	100,000
OP (1)	158	2,117	2,677	301	3,233	3,883	846	10,486	17,547	2,927	33,592	88,528
F (4)	37	1,143	1,381	61	1,256	1,687	184	3,160	5,011	744	9,438	23,798
C (4)	68	893	949	129	1,096	1,288	520	4,346	6,067	2,576	16,239	30,501
M (4)	43	710	811	95	896	1,135	479	3,626	5,358	2,518	13,172	27,399
G (4)	41	491	636	74	674	1,052	249	3,832	6,280	1,105	13,070	34,983
F (8)	19	790	1,008	34	898	1,136	95	1,880	2,843	394	4,924	12,610
C (8)	40	493	524	91	640	771	474	2,814	3,687	2,508	11,039	18,558
M (8)	27	411	463	70	539	676	450	2,467	3,351	2,458	9,623	17,063
G (8)	21	263	336	37	352	551	132	1,956	3,205	580	6,653	17,713
F (16)	10	649	809	19	700	867	53	1,255	1,812	223	3,003	6,922
C (16)	25	288	308	67	413	473	445	2,063	2,522	2,447	8,537	12,701
M (16)	20	247	270	58	370	428	432	1,953	2,355	2,429	8,114	11,882
G (16)	10	136	171	19	181	283	72	1,063	1,651	319	3,457	9,125
F (32)	9	599	745	16	632	748	46	1,094	1,450	152	2,405	4,009
C (32)	18	174	187	55	289	324	479	1,705	1,985	3,014	7,543	10,041
M (32)	17	168	190	50	286	313	440	1,674	1,999	2,782	7,897	9,566
G (32)	7	83	114	15	127	188	63	567	962	223	2,001	4,814

OP indicates the sequential OmegaPlus implementation; F, C, M, and G indicate the fine-grained, coarse-grained, multi-grained, and generic parallel algorithms, respectively. The number in parentheses is the number of threads

ISSN: 2047-217X