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Table 2 Comparison of MEC and runtimes for different schemes applied to Fosmid data

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

chr # Fosmid
  CPLEX SDhaP RefHap HAPCUT HapTree
  MEC t(in secs) MEC t(in secs) MEC t(in secs) MEC t(in secs) MEC t(in secs)
1 6889 480 7297 8.07 8051 2.61 9550 600 9676 6501
2 6700 451 7214 7.84 7910 2.65 9661 660 9802 7196
3 5122 420 5588 6.49 6111 2.969 7557 360 7705 4847
4 4072 360 4510 5.41 4880 1.81 6265 540 6500 8392
5 4637 762 5029 6.2 5558 2.15 6919 480 7094 5670
6 5248 471 5674 7.26 6341 2.093 7958 2700
7 4174 464 4509 5.02 4961 2.07 6062 480 6169 5589
8 4301 347 4785 5.09 5092 2.0 6255 615 6379 8316
9 3974 191 4200 4.7 4591 1.76 5463 376 5513 4465
10 4508 270 4765 5.04 5357 2.52 6445 454 6553 4838
11 3903 150 4165 4.63 4620 2.23 5558 457 5625 5183
12 3907 159 4174 5 4686 2.18 5654 360 5770 5654
13 2669 137 2946 3.0 3155 1.1 3967 291 4029 5367
14 2814 413 2971 3.35 3244 1.89 3978 302 4038 4103
15 2903 138 3029 3.09 3341 1.54 4007 250 4116 3357
16 3844 221 4022 4.84 4438 1.66 5086 570 5142 9683
17 3448 295 3586 3.41 4159 1.86 4743 251 4806 3003
18 2337 288 2555 2.69 2801 1.39 3445 240 3493 2303
19 2707 70 2857 2.78 3406 1.35 3898 180 3953 1984
20 2783 305 2943 3.08 3295 1.72 3810 203 3886 1529
21 1367 72 1452 1.44 1601 1.05 1951 134 1979 1410
22 2422 175 2508 3.21 2876 1.69 3260 118 3307 1351
  1. MEC and running times for CPLEX, SDhaP, HAPCUT, RefHap and HapTree haplotype assembly strategies applied to Fosmid data. SDhaP is more accurate than the other schemes except CPLEX and significantly faster than HapCUT or HapTree. For chromosome 6, HapTree did not complete its run within 48 hours and hence the corresponding entry is missing.