Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data

Table 3 Performance comparison of MCF7 RRBS reads

	TRACE-RRBS	BISMARK	BRAT-BW	BS-SEEKER2	BSMAP	METHYL-CODER	NOVO-ALIGN	LAST
Run Time (hours)^a	3.2	10.89	9.1	3.6	3.19	14.4	24.5	11.2
Memory Usage (GB)	8.4	12.69	2.78	5.3	6.1	18.76	13	16.1
%Unique Reads	49.4	48.1	40.7	48.5	49.6	41.2	49.5	45.5
#C@10X (million)	2.38	1.87	NA	1.98	2.11	2.72	2.14	2.41
Correlation with 450 K chip (R²)	0.95	0.91	NA	0.95	0.91	0.64	0.91	0.84

ISSN: 1471-2164