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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

From: A comparison of topologically associating domain callers over mammals at high resolution

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 = ā€˜Gā€™; 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