Table 1 Performance of KSNP and the four state-of-the-art haplotyping tools on PacBio CLR and HiFi datasets

Dataset^22,25	Tool^a	SE (%)	HE (%)	Hap N50 (kb)	Recall (%)	CPU time (s)	Wall time (s)	RAM (MB)
HG001 CLR 50×	Longshot	0.63	1.14	239	91.56	13,485	14,186	2970
	WhatsHap	0.67	1.57	241	91.61	20,714	22,050	1843
	HapCUT2	0.67	1.84	251	91.66	6100	6478	969
	Margin	0.63	0.89	171	90.30	146,551	19,283	2867
	KSNP^a	0.68	1.82	246	91.59	1881	2004	510
HG002 CLR 50×	Longshot	1.22	1.53	315	89.86	13,537	14,267	2662
	WhatsHap	1.25	2.03	317	89.91	19,141	19,963	1536
	HapCUT2	1.25	2.25	324	89.95	6042	6453	802
	Margin	1.21	1.38	244	89.17	128,479	16,471	2458
	KSNP	1.25	2.12	321	89.91	1607	1740	476
HG002 HiFi 50×	Longshot	1.26	1.21	416	93.67	11,285	11,982	2458
	WhatsHap	1.27	1.48	417	93.68	13,254	13,880	1229
	HapCUT2	1.27	1.41	417	93.68	5125	5483	685
	Margin	1.26	1.17	370	93.42	112,980	15,064	2253
	KSNP	1.27	1.46	422	93.68	1106	1270	462
HG005 CLR 50×	Longshot	1.45	2.77	490	92.75	17,968	18,865	2765
	WhatsHap	1.49	4.01	507	92.80	22,968	24,093	1434
	HapCUT2	1.49	4.43	528	92.84	8202	8659	946
	Margin	1.44	2.40	315	91.23	145,455	18,648	2253
	KSNP	1.49	3.98	514	92.80	2088	2268	513
HG01109 CLR 40×	Longshot	0.04	4.92	5080	89.61	20,794	21,930	2662
	WhatsHap	0.06	5.42	5323	89.66	22,919	23,917	1331
	HapCUT2	0.07	6.11	5717	89.67	9615	10,184	849
	Margin	0.03	2.46	3804	89.47	125,506	16,513	2355
	KSNP	0.07	5.94	5333	89.66	1304	1449	512
A.thaliana CLR 45×	Longshot	0.01	2.59	4001	85.97	3570	3586	911
	WhatsHap	0.01	2.12	4001	85.98	2610	2655	615
	HapCUT2	0.01	2.43	4001	85.99	1753	1759	392
	Margin	0.01	2.07	1228	85.37	9619	1202	2150
	KSNP	0.01	2.56	4001	85.98	100	100	152

SE switch error rate, HE hamming error rate, Wall time wall clock time, RAM peak RAM.
^aLongshot, WhatsHap, HapCUT2, and KSNP were performed with one thread in the experiments, while Margin utilized eight threads. The k value in KSNP was set to two by default.

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