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Table 1 Performance comparison of AltHap, H-PoP, BP, HapTree, SCGD, and ILP applied to haplotype reconstruction of the CEU NA12878 data set in the 1000 Genomes Project

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 97.4 2011 11.26 95.7 2264 5.22 99.1 2321 8.17
2 95.3 2562 12.22 95.6 2971 5.65 89.5 2897 9.83
3 93.3 2084 10.38 91.2 2312 6.99 74.3 2367 8.30
4 96.9 2368 12.16 97.0 2648 5.24 74.8 2613 6.76
5 97.2 1924 9.96 96.6 2103 4.67 88.2 2185 4.76
6 94.9 3687 14.17 95.2 3343 4.93 88.7 3588 6.94
7 97.0 1846 11.19 92.4 1986 4.24 81.1 2073 7.88
8 96.2 1634 9.63 94.7 1848 4.14 88.5 1857 8.01
9 97.1 1272 6.42 91.0 1462 3.36 89.8 1491 6.13
10 96.8 1584 7.97 94.5 1683 3.67 90.8 1839 7.18
11 93.3 1394 7.45 91.5 1553 3.71 75.6 1586 6.69
12 92.1 1423 7.12 90.3 1570 3.46 74.4 1589 6.48
13 97.0 1269 4.42 94.1 1440 2.89 89.1 1409 5.38
14 90.3 857 9.53 97.1 974 2.54 70.0 995 4.53
15 97.2 941 9.42 97.4 1039 2.40 74.6 1063 3.92
16 96.7 1198 5.40 93.5 1192 2.47 79.7 1269 4.42
17 97.5 1146 4.58 91.1 1244 1.98 92.4 1234 3.15
18 91.0 860 4.54 97.6 893 2.51 82.0 942 3.79
19 97.6 618 3.32 97.8 695 1.82 98.0 1060 2.47
20 97.3 703 3.53 95.0 719 2.00 97.1 796 2.74
21 97.4 470 2.51 97.0 512 1.70 97.5 532 1.86
22 97.3 367 1.98 98.3 427 1.44 90.7 438 1.72
Mean 95.8 1464 7.69 94.8 1585 3.50 85.0 1643 5.51
Sd 2.27 780 3.54 2.54 790 1.49 8.94 793 2.32
# best 9 0 0 5 0 5 3 0 0
  HapTree SCGD ILP
Chromosome CPR MEC t(sec) CPR MEC t(sec) CPR MEC t(sec)
1 84.1 2305 15.43 92.5 2456 3.62 95.6 1741 173.68
2 84.5 2875 17.59 92.6 3509 4.41 95.3 2219 190.37
3 85.2 2363 15.06 91.9 2498 3.40 95.6 1788 152.09
4 83.5 2604 18.67 92.7 3754 5.47 97.1 2048 168.56
5 84.8 2171 16.95 93.9 2750 3.54 95.4 1691 147.72
6 84.6 3583 23.86 93.0 5612 8.70 95.7 2643 181.51
7 84.7 2070 13.06 93.5 2826 3.95 95.4 1590 133.36
8 84.2 1838 14.81 90.7 1692 2.18 95.6 1472 136.60
9 85.1 1479 14.90 97.1 1885 2.94 95.2 1125 105.34
10 85.7 1823 12.13 92.6 1876 2.56 95.7 1354 120.89
11 83.6 1577 11.33 93.2 2265 2.95 95.2 1206 104.74
12 84.8 1589 9.97 92.3 1612 2.03 95.4 1214 103.88
13 82.8 1405 9.55 97.0 2947 3.31 95.5 1105 93.33
14 85.4 987 7.79 91.1 904 1.36 95.3 752 65.07
15 83.6 1061 7.43 99.1 1041 1.21 94.1 809 66.52
16 85.1 1273 8.13 93.0 1305 1.79 95.5 920 77.81
17 84.8 1230 6.34 96.7 2123 2.61 96.1 943 47.99
18 84.1 941 7.13 90.3 933 1.16 95.2 720 71.49
19 84.6 765 5.26 97.2 1290 3.25 96.6 533 44.32
20 86.9 795 6.08 96.8 949 1.38 95.8 612 54.30
21 86.3 528 5.05 94.3 499 0.63 95.2 415 31.82
22 86.9 436 4.65 94.1 422 0.74 95.2 316 31.89
Mean 84.8 1623 11.42 93.9 2052 2.87 95.5 1237 104.69
Sd 1.03 802 5.23 2.3 1222 1.80 0.57 612 50.37
# best 0 0 0 1 0 17 5 22 0
  1. The best results in each Chromosome and in all Chromosomes are in bolface font