§	Analysis	Data	Reference	Agreement	Verdict
1	Diamond insulation	mouse Hi-C, 10 kb, window 100 kb	cooltools 0.7.1	max |difference| 5.1e-06 over 250,342 bins; the same 11,089 boundaries	Identical (float32)
2	Directionality index	mouse Hi-C, 50 kb, window 2 Mb	domaincaller 0.1.0	max relative difference 5.0e-06 over 48,094 bins; every sign agrees	Identical (float32)
3	Compartments	mouse Hi-C, 100 kb, GC-phased	cooltools 0.7.1	E1 1 − r ≤ 1e-12 on 20 chromosomes, no bin more than 5e-06 apart; eigenvalues within 1e-06; A/B ≥ 100.00%	Same eigenvectors
4	P(s)	yeast Micro-C 800 bp; mouse Hi-C 10 kb	cooltools 0.7.1	max relative difference 3.7e-06 over 153 points	Identical (float32)
5	Peak calling (yapc, IDR)	mouse ATAC-seq, 2 replicates, chr19	yapc 0.1, idr 2.0.3	100,000 regions, same bounds and summits; 5,666 peaks at IDR ≤ 0.05; −log10 IDR within 8.7e-04 of 5 yapc seeds (seeds among themselves: up to 8.7e-04)	Identical peaks; IDR within yapc's seed-to-seed spread
6	Loops (chromosight)	yeast Micro-C, 800 bp	chromosight 1.6.3	659 loops, the same bin pairs; scores within 5.1e-07	Identical
7	Reproducibility (HiCRep)	chicken Hi-C, 3 maps, 100 kb, raw counts	hicrep 0.2.6	within 5.0e-05 over 78 values (4 decimals written)	Identical
8	3D model (pastis-NB)	yeast Micro-C, 12.8 kb, 905 beads	pastis 0.5.0 (GitHub 6888ac2)	same seed: within chromosomes ρ = 0.978–0.993, between 0.90–1.00 (pastis vs pastis 0.940–0.949, 0.50–0.57); fit within chromosomes 0.866–0.871 vs 0.868–0.873, all pairs 0.473–0.480 vs 0.473–0.480	Same seed, same model; fits within chromosomes as well as pastis; all pairs as well as pastis
9	Coverage	mouse Hi-C, 10 kb, raw and balanced	cooltools 0.7.1	raw: identical on 272,564 bins, cooltools' diagonal counted once; balanced within 5.0e-06	Identical
10	Virtual 4C	mouse Hi-C, 10 kb, three viewpoints, whole genome	cooltools 0.7.1	every bin cooltools reports (1,099) within 4.5e-06; the others 0 or the viewpoint	Identical (float32)
11	Aggregate peak analysis	mouse Hi-C, 10 kb, 2,515 loops	coolpuppy 1.1.0	raw and over the expected, at coolpuppy's defaults and with every loop, and on the diagonal: the same cells left as gaps, every other cell within 4.5e-06; over controls, two runs of the two tools differ as two of coolpuppy do (0.134 against 0.151), and no more cells than chance gives (1 of 121 at p < 0.01)	Identical (float32); controls within the seeds' spread
12	APA, chromosight's score	mouse Hi-C, 10 kb, 2,515 loops	chromosight 1.6.3	2,515 loops scored, within 5.0e-05; pileup within 4.8e-06	Identical
13	Boost-HiC	mouse Hi-C, 100 kb, chr19, chr11, chr1	Boost-HiC (GitHub a615aff)	the same bins kept; 5,404,076 cells within 5.0e-10	Identical
14	Metaplot	mouse ATAC-seq, one and two replicates, whole genome, RefSeq TSS ±2 kb	deepTools 4.0.0	profiles within 4.7e-06; 35,034 rows a track, paired one to one within the rounding; over two tracks, plotHeatmap's order	Identical
15	Interval overlap	ATAC-seq peaks (§ 5) and promoters, chr19	bedtools 2.31.1	the same bases and features counted; the nulls' means within 0.3 standard errors	Identical; the same null
16	Base composition	mm10, 10 kb bins	bioframe 0.8.0, Biopython 1.88	GC within 7.2e-08, skew within 6.7e-08 over 264,952 bins	Identical (float32)
17	Motif search	mm10 chr19, two motifs, both strands	seqkit 2.3.0	the same 199,858 and 145,681 sites	Identical
18	Track correlation	mouse ATAC-seq, two replicates, and insulation, chr19, 100 bp to 10 kb windows	pyBigWig 0.3.26 and SciPy 1.16.3; deepTools 4.0.0	18 coefficients within 4.5e-07 of the exact means, a window any track lacks left out of every pair as deepTools leaves it; deepTools within 0.027, from its zoom-level means	Identical to the exact means
19	Loop calling	mouse Hi-C, 10 kb, every chromosome	cooltools 0.7.1	236 loops, the same bin pairs, contacts and clusters; λ within 5.0e-05, q within 5.0e-05, the digits written	Identical (to the digits written)
20	Cis and trans per sequence	chicken Hi-C, 100 kb, 36 sequences, raw and balanced	cooltools 0.7.1	raw: the same contacts within and between every sequence; balanced: the pairs within 4.6e-06; against indifference within 4.6e-06 of NumPy over cooltools' sums	Identical (to the digits written)
21	Saddle	mouse Hi-C, 100 kb, § 3's E1, 20 chromosomes	cooltools 0.7.1	every cell within 5.0e-06, the corners within 4.9e-03	Identical (float32)
22	Fraction of signal in features	mouse ATAC-seq, 2 replicates, chr19; § 5’s peaks and § 15’s promoters	pyBigWig 0.3.26, NumPy 2.5.4	every feature's signal and mean to the digits written; inside, the exact sum; the whole track, from a zoom level, within 4.8e-05; FRiP within 4.5e-05	The same FRiP to its four decimals and every feature to the digits written, the whole track read from a zoom level
23	Signal by group	mouse ATAC-seq, 2 replicates, chr19, by § 3's compartments; one value per entry, and 10 kb stretches	pyBigWig 0.3.26, NumPy 2.5.4, SciPy 1.16.3	the same entries and stretches, their means within 5.0e-06; every one of the summaries and tests as written	Identical (to the digits written)
24	CTCF sites in GM12878 (Fig. 2)	GM12878 Hi-C, 10 and 2 kb; CTCF ChIP-seq of two labs and ATAC-seq; chr19	cooltools 0.7.1, yapc 0.1, coolpuppy 1.1.0, deepTools 4.0.0	insulation at four scales within 5.0e-06, the same 306 boundaries; the same 2,106 peaks at IDR ≤ 0.05, −log10 IDR within 1.9e-05 (seeds among themselves: up to 2.3e-05); APA over 2,105 consecutive pairs within 4.9e-06; metaplots within 4.8e-06, 0 cells past the rounding	Identical (float32); IDR within yapc's seed-to-seed spread
25	Pairs statistics	yeast Hi-C contact list, deduplicated	pairtools 1.1.2	every key, and every value as the file spells it	Identical
26	Restriction sites	yeast R64-1-1, DpnII, 5 kb bins	bioframe 0.8.0, Biopython 1.88	the same 35,896 cuts, bioframe's 2 bp later; the same number of cuts in every one of the 2,441 bins	Identical
27	Pairs QC	§ 25's contact list against § 26's DpnII sites, 5 kb	pairtools 1.1.2, cooler 0.10.4, cooltools 0.7.1	classes, distances, fragments seen and coverage the same, key for key; ρ 0.482 against 0.4823; every one of its statistics as pairtools writes it	Identical
28	TAD annotation	K562 Hi-C (.hic), chromosomes 21 and 22, 10 kb, raw and KR	Juicer Tools 1.22.01	200 domains (balanced) and 177 (raw), the same corners; scores within 5.0e-07, the digits written	Identical (to the digits written)
29	Map report	yeast Micro-C, every stored resolution	cooler 0.10.4, numpy	10 resolutions, bins, mean, median, 80 % count and shares, the digits written	Identical (to the digits written)