S-conLSH: alignment-free gapped mapping of noisy long reads

BMC Bioinformatics

Table 3 Comparative study of the number of correct mappings, sensitivity, precision, and running time by different methods, Minimap, Minimap2, lordFAST, MUMmer4, conLSH, and S-conLSH, for a total of 146,932 reads simulated from five different human chromosomes

Chr#	#Reads	Mapper	#Mapped reads	#Correct mapping	Sensitivity (%)	Precision (%)	Indexing time (s)	Mapping time (s)
Chr1	32,290	Minimap	31,591	31,585	97.82	99.99	15	30
		Minimap2	32,290	31,863	98.69	98.69	10	61
		lordFAST	32,290	29,313	90.79	90.79	192	206
		MUMmer4	31,940	31,645	98.01	99.08	-	310
		conLSH	31,945	29,620	91.73	92.72	08	235
		S-conLSH	32,111	31,964	99	99.55	51	38
Chr2	34,309	Minimap	33,623	33,613	97.98	99.98	16	33
		Minimap2	34,309	33,864	98.71	98.71	10	64
		lordFAST	34,309	31,173	90.87	90.87	170	216
		MUMmer4	34,056	33,914	98.85	99.59	-	312
		conLSH	34,082	31,230	91.03	91.63	10	229
		S-conLSH	34,153	34,008	99.13	99.58	54	44
Chr3	28,109	Minimap	27,481	27,477	97.76	99.99	15	25
		Minimap2	28,109	27,698	98.55	98.55	8	52
		lordFAST	28,109	25,513	90.77	90.77	135	167
		MUMmer4	27,894	27,791	98.87	99.64	-	253
		conLSH	27,899	25,603	91.08	91.77	07	198
		S-conLSH	27,957	27,863	99.13	99.67	45	30
Chr4	26,871	Minimap	26,307	26,301	97.88	99.98	16	23
		Minimap2	26,871	26,501	98.63	98.63	8	51
		lordFAST	26,871	24,403	90.82	90.82	129	158
		MUMmer4	26,638	26,533	98.75	99.61	-	248
		conLSH	26,650	24,449	90.98	91.74	07	180
		S-conLSH	26,748	26,650	99.18	99.64	41	29
Chr5	25,353	Minimap	24,859	24,849	98.02	99.96	14	21
		Minimap2	25,353	25,056	98.84	98.84	7	48
		lordFAST	25,353	23,069	91	91	123	149
		MUMmer4	25,126	24,951	98.42	99.31	-	234
		conLSH	25,149	23,106	91.14	91.87	06	167
		S-conLSH	25,242	25,155	99.22	99.66	39	23

ISSN: 1471-2105