BMC Genomics

Table 1 Comparison of MEC and runtimes for different schemes applied to HuRef data

From: SDhaP: haplotype assembly for diploids and polyploids via semi-definite programming

chr #	Huref
	CPLEX		SDhaP		HAPCUT		RefHap		HapTree
	MEC	t(in secs)	MEC	t(in secs)	MEC	t(in secs)	MEC	t(in secs)	MEC	t(in secs)
1	16853	1.72×10⁵	17192	190	19777	251	18739	8354	21112	8499
2	12618	1260	12713	220	14698	185	13762	3576	15720	8210
3	9296	960	9444	153	10714	257	10096	4866	11424	12183
4	9958	1140	10106	115	11567	274	10936	5399	12479	9534
5	9195	1080	9333	141	10590	196	10045	4398	11391	8972
6	8637	900	8696	105	9922	247	9318	4225	10912	8462
7	9782	1020	9954	102	11279	152	10540	7030	12196	6876
8	8480	3960	8604	90	9832	226	9352	4640	10552	9162
9	8051	780	8134	88	9290	111	8850	3898	9905	5515
10	8550	1200	8680	87	9877	209	9323	5203	10598	8782
11	7027	840	7186	92	8210	156	7744	4514	8856	7093
12	7136	720	7256	100	8240	152	7725	2669	9003	5494
13	5090	600	5142	62	5844	125	5511	3363	6285	7680
14	5086	480	5173	52	5861	72	5537	2313	6273	3533
15	8088	1.67×10⁵	8216	71	9364	108	9031	2014	10218	4018
16	7176	1500	7231	51	8287	138	7830	1896	8769	4589
17	5739	480	5819	47	6570	86	6238	2362	7106	5626
18	4403	540	4467	56	5041	108	4814	1542	5500	3544
19	4628	480	4670	32	5335	65	5052	1132	5660	2804
20	3243	300	3316	37	3753	63	3458	1472	4068	3602
21	3360	2400	3369	31	3914	63	3752	739	4154	1692
22	3908	7.16×10⁵	3973	32	4539	43	4384	1786	4780	1683

MEC and running times for CPLEX, SDhaP, HAPCUT, RefHap and HapTree algorithms applied to HuRef data. SDhaP is more accurate than all schemes except for CPLEX (which is the only one that requires proprietary software). However, for longer blocks, the complexity of the CPLEX scheme may become very high as evident from chromosomes 1, 15 and 22.

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ISSN: 1471-2164

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