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Table 3 Performance comparison of AltHap, H-PoP, BP, HapTree, SCGD, and ILP on a simulated diploid data set from [39] with haplotype block length m=700. ILP could only finish assembly of haplotypes for two settings in 48 hours

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

   AltHap H-PoP BP
Error rate Coverage CPR MEC t(s) CPR MEC t(s) CPR MEC t(s)
0.1 5 99.6 477 0.043 99.3 402 0.012 86.7 698 1.421
0.1 8 99.9 759 0.128 99.8 780 0.035 87.2 861 4.627
0.1 10 99.9 954 0.404 99.9 903 0.109 87.3 1130 13.58
0.2 5 90.9 941 0.061 87.7 1021 0.027 81.2 953 2.671
0.2 8 98.1 1458 0.141 88.9 1532 0.098 86.1 1847 6.897
0.2 10 99.1 1836 0.394 91.5 2023 0.201 86.7 2485 10.13
0.3 5 60.7 1228 0.069 61.8 1331 0.041 53.7 1677 3.235
0.3 8 67.7 2022 0.145 65.7 2250 0.098 57.2 2469 7.982
0.3 10 75.0 2558 0.375 71.2 2979 0.217 59.6 3114 15.32
   HapTree SCGD ILP
Error rate Coverage CPR MEC t(s) CPR MEC t(s) CPR MEC t(s)
0.1 5 88.6 491 2.13 96.6 523 0.66 98.8 467 471
0.1 8 88.4 767 3.82 99.8 772 0.84 99.7 760 2004
0.1 10 87.3 963 4.03 99.9 965 0.97 - - -
0.2 5 76.2 988 9.36 76.1 979 0.72 - - -
0.2 8 80.8 1562 6.69 91.3 1531 1.18 - - -
0.2 10 82.7 1943 4.20 95.4 1902 1.50 - - -
0.3 5 64.6 1170 10.21 57.8 1136 0.73 - - -
0.3 8 65.7 2021 6.17 63.7 1998 1.14 - - -
0.3 10 65.1 2597 5.74 67.9 2574 1.44 - - -
  1. The best results in each simulation setting are in bolface font