Table 9.
Running time of different TAD callers at 5kb resolution for chromosome 6 on human embryonic stem cell line, tested over a 2.9 GHz 8-Core Intel i9 cpu having 128 GB memory
| Methods | Key Parameters | Running time (s) |
|---|---|---|
| Armatus | g = 0.5 | 90.76 |
| Arrowhead | Normalization = KR | 92.93 |
| CaTCH | Defaults | 44.19 |
| Constrained HAC | h = 342 | 26.48 |
| CHDF | length = 3422; number = 3422; size = 342 | 952.38 |
| ClusterTAD | Max_TADsize = 800000 | 7608.69 |
| deDoc | Defaults | 264.85 |
| DI | window = 2500000; min = 2; prob = 0.99 | 294.77 |
| EAST | Defaults | 11.28 |
| GMAP | Defaults | 62.46 |
| GRiNCH | Defaults | 22.57 |
| HiCExplorer | minDepth = 3*50000; maxDepth = 6*50000; step = 50000 | 22.94 |
| HiCKey | Defaults | 42.13 |
| HiCseg | change_max = 342; distrib = ‘G’; | 146.32 |
| IC-Finder | Defaults | 64.49 |
| InsulationScore | is = 2500000; ids = 1000000; im = mean; bmoe = 3; nt = 0.1 | 474.39 |
| Matryoshka | g = 0.5 | 123.95 |
| MrTADFinder | res = 1.5 | 625.73 |
| MSTD | MDHD = 10; window = 10 | 16.48 |
| OnTAD | Defaults | 4.78 |
| Spectral | Threshold = 0.8; region size = 1 | 61.69 |
| SpectralTAD | levels = 2 | 32.15 |
| TADBD | Defaults | 19.19 |
| TADbit | Defaults | 20910.81 |
| TADpole | Defaults | 211.63 |
| TADtree | S = 50; q = 12; p = 3; M = 10; N = 1025; gamma = 500 | 32732.71 |
| TopDom | w = 5 | 28.43 |