GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists

GigaScience

Table 1 Comparison of the 32-mer counting speeds of GenomeTester4, Jellyfish 2.2.0, KMC 2.2 and DSK 2.0.7 with a single thread and 24 threads

		E. coli K-12 strain MG1655 genome	H. sapiens genome	S. aureus sequencing reads (GAGE library 1)	H. sapiens chromosome 14 sequencing reads (GAGE library 1)
File sizes		1 file, 4.7 Mbp	24 files, 3.0 Gbp	2 files, 86 Mbp	2 files, 2.55 Gbp
1 thread	GListMaker	0.9	978.47	16.61	764.17
	JellyFish	3.64	1923.99	43.1	1222.48
	KMC	0.76	354.32	11.22	338.52
	DSK	2.52	102.41	14.41	361.50
24 threads	GListMaker	1.52	243.44	12.15	261.7
	JellyFish	0.54	112.52	5.65	100.84
	KMC	0.25	41.47	2.48	57.19
	DSK	2.63	60.76	3.51	59.16

All measurements are taken as the mean of five runs and presented in seconds. For KMC, the RAM-only version was used to speed up the counting; for DSK the RAM limit was 200 GiB

ISSN: 2047-217X