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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