Table 1.

Comparison of FastHap with Greedy and HapCut in terms of accuracy (MEC) and execution time using HuRef dataset. Best results in each column showed in bold

	Time (min)			Speedup using FastHap		MEC (accuracy performance)
Chr	Greedy	HapCut	FastHap	versus Greedy	versus HapCut	Greedy	HapCut	FastHap
1	606	880	183	3.3	4.8	29 657	19 750	19 423
2	1001	2446	149	6.7	16.4	22 980	14 677	14 220
3	1809	1053	188	9.6	5.6	16 878	10 738	11 794
4	542	694	63	8.6	11.0	18 153	11 931	11 812
5	1381	3229	282	4.9	11.4	16 590	10 630	10 362
6	681	750	109	6.2	6.9	15 587	9992	9870
7	456	604	76	6.0	7.9	17 402	11 290	11 245
8	5052	4514	334	15.1	13.5	14 887	9845	10 830
9	2006	1747	293	6.8	6.0	13 812	9318	9204
10	667	1445	170	3.9	8.5	15 291	9906	9796
11	332	288	69	4.8	4.2	12 906	8294	8091
12	1303	1638	165	7.9	9.9	12 630	8297	7467
13	428	761	158	2.7	4.8	9312	6131	6143
14	3315	1919	383	8.7	5.0	9734	6360	5725
15	907	1137	208	4.4	5.5	13 988	9783	9695
16	157	248	42	3.7	5.9	12 621	8354	8215
17	2223	2790	246	9.0	11.3	11 157	7398	7386
18	698	798	87	8.0	9.2	8578	5043	4846
19	309	501	41	7.5	12.2	8214	5497	4886
20	326	348	32	10.2	10.9	5752	3784	3437
21	482	154	48	10.0	3.2	6611	4715	4707
22	535	128	39	13.7	3.3	8295	5864	5875
Overall	25 217	28 074	3365	7.4	8.1	301 035	197 597	195 029
	Sum over all chromosomes			Average		Sum over all chromosomes

Note. FastHap achieves speedups of 16.4 and 15.1 compared with HapCut and Greedy, respectively, is 1.9 and 35.4% more accurate than HapCut and Greedy, respectively. Statistics on coverage and haplotype length are shown in Figs 2 and 3 and further discussed in Section 3.2.