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Table 2 Performance comparison of AltHap, H-PoP, BP, HapTree, SCGD, and ILP applied to the Fosmid data set. HapTree could not finish assembling haplotype of the 6th chromosome in 48 hours

From: Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids

  AltHap H-PoP BP
Chromosome CPR MEC t(sec) CPR MEC t(sec) CPR MEC t(sec)
1 95.5 9731 18.38 84.8 9845 2.13 87.6 9567 40.18
2 95.5 9589 38.89 90.4 9444 2.16 84.8 9698 42.90
3 91.7 7311 29.40 91.7 7182 1.79 84.7 7587 30.61
4 92.7 5508 26.69 92.6 5775 1.76 86.9 6288 31.10
5 92.0 6711 27.39 93.9 6910 1.95 86.3 6975 36.94
6 90.9 7213 33.68 88.5 7505 2.40 85.0 7590 41.20
7 90.7 6151 28.60 91.9 6829 1.68 85.8 6091 36.94
8 91.2 5927 23.82 90.2 6143 1.89 87.3 6282 38.87
9 91.8 5347 19.40 91.8 5719 1.76 85.1 5493 26.13
10 90.1 6044 24.07 92.4 6328 1.48 86.4 6503 27.65
11 90.8 5424 21.73 90.3 6432 1.68 85.8 5579 20.56
12 91.5 5456 24.25 91.4 5653 1.46 85.0 5706 24.19
13 90.4 3646 14.23 90.1 3708 1.54 82.7 3976 17.33
14 89.5 4156 18.64 89.1 4261 1.21 87.0 4004 14.84
15 90.0 4079 14.67 72.9 4001 1.06 82.3 4022 14.35
16 88.5 6197 26.28 71.5 6119 1.20 84.4 5112 29.51
17 89.7 4507 16.35 88.3 4911 1.22 87.6 4749 18.29
18 93.0 3080 12.68 90.8 3315 1.14 85.5 3457 13.31
19 85.7 4212 13.40 86.3 4115 0.84 83.5 3928 13.44
20 90.3 3512 13.64 90.0 4121 0.85 84.9 3814 15.97
21 92.7 1871 6.20 91.9 1974 0.68 87.2 1953 8.18
22 85.1 3654 17.24 87.8 3757 0.62 86.7 3910 14.72
mean 90.9 5424 21.35 88.6 5639 1.48 85.6 5558 25.33
Sd 2.5 1950 7.79 5.7 1934 0.50 1.5 1948 10.84
# best 13 0 0 4 0 9 0 0 0
  HapTree SCGD ILP
Chromosome CPR MEC t(sec) CPR MEC t(sec) CPR MEC t(sec)
1 91.5 9676 6501 95.1 10127 2.59 79.0 6889 80.33
2 92.3 9802 7196 94.5 9721 2.41 76.1 6700 76.60
3 90.7 7705 4847 88.6 7410 1.83 76.9 5122 79.50
4 90.8 6500 8392 87.6 5494 1.48 77.0 4072 51.49
5 90.8 7094 5670 89.6 7058 1.71 76.0 4637 54.39
6 - - - 90.4 7843 2.14 75.7 5248 63.37
7 91.5 6169 5589 89.4 6189 1.73 77.9 4174 46.85
8 91.2 6379 8316 87.4 5996 1.47 76.3 4301 53.57
9 91.7 5513 4465 90.0 5592 1.20 76.8 3974 42.41
10 88.9 6553 4838 92.8 6027 1.60 76.8 4508 59.25
11 90.5 5625 5183 90.1 5662 1.34 79.0 3903 45.45
12 91.3 5770 5654 90.5 5731 1.55 77.5 3907 48.76
13 89.8 4029 5367 87.6 3727 0.79 77.1 2669 32.09
14 90.6 4038 4103 92.9 4859 1.12 75.4 2814 39.61
15 90.7 4116 3357 87.8 4442 0.88 78.7 2903 33.80
16 94.2 5142 9683 95.5 6474 1.60 79.8 3844 62.44
17 93.1 4806 3003 97.1 4843 1.01 80.8 3448 42.00
18 91.9 3493 2303 88.3 3478 0.71 76.9 2337 32.27
19 92.8 3953 1984 82.5 4204 0.87 78.6 2707 33.68
20 90.1 3886 1529 94.6 3790 0.83 78.7 2783 31.78
21 92.1 1979 1410 90.7 2042 0.36 77.2 1367 16.42
22 92.4 3307 1351 90.6 3495 1.06 77.0 2422 60.62
mean 91.4 5502 4797.19 90.6 5645 1.38 77.6 3851 49.39
Sd 1.2 1998 2392.54 3.4 1977 0.56 1.39 1360 16.82
# best 4 0 0 4 0 13 0 22 0
  1. The best results in each Chromosome and in all Chromosomes are in bolface font