SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores

BMC Bioinformatics

Table 5 Time usage details of SWAP-Assembler's five steps on processing three small datasets using a share memory machine with 32 cores.

	Steps	4 cores	8 cores	16 cores	32 cores
S. aureus	input parallelization & graph construction	31.29	16.32	9.55	4.91
	graph cleaning	2.14	1.07	0.6	0.3
	graph reduction	45.75	24.2	13.23	7.67
	contig extension	1.54	0.89	0.6	0.52
R. sphaeroides	input parallelization & graph construction	49.19	26.42	14.88	7.79
	graph cleaning	3.63	1.99	0.97	0.54
	graph reduction	73.78	39.31	20.83	12.19
	contig extension	2.37	1.33	0.85	0.64
Hg14	input parallelization & graph construction	628	327	184	98
	graph cleaning	71	37	19	10
	graph reduction	1328	734	413	242
	contig extension	140	89	69	58

ISSN: 1471-2105