biobambam: tools for read pair collation based algorithms on BAM files

Table 5 Run-time comparison of bammarkduplicates2 and alternatives on compute farm nodes (part a)

Run-time comparison for BAM duplicate marking on server blades
Data set	Program	Memory/GB	Run-time/minutes
HG03520	biobambam	0.33	5.86±0.42
	Picard	7.96	13.80±0.18
	bamUtil	0.030	5.57±0.37
ERR239642	biobambam	0.37	13.37±0.51
	Picard	9.26	26.25±0.30
	bamUtil	0.092	13.18±0.35
ERR217514	biobambam	0.39	34.22±0.58
	Picard	13.15	46.15±0.61
	bamUtil	0.19	33.85±0.53
ERR196957	biobambam	0.45	52.43±0.92
	Picard	11.53	90.74±1.00
	bamUtil	0.47	52.45±1.56
HG00096	biobambam	0.43	78.76±0.99
	Picard	13.95	126.64±1.37
	bamUtil	0.35	76.18±1.96

Run-time comparison of biobambam’s bammarkduplicates2, Picard’s MarkDuplicates and bamUtil’s dedup for the data sets HG03520, ERR239642, ERR217514, ERR196957 and HG00096 described in Table2 on compute farm nodes.

ISSN: 1751-0473