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 |