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
| Â | Â | 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 |
| Â | Â | 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 | - | - | - |