RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads

BMC Bioinformatics

Table 5 Statistics of running time and memory consumption of each tools on five datasets

Species	Method	User time (s)	System time (s)	Percent of CPU this job got (%)	Maximum resident set size (kbytes)	File system outputs
Drosophila melanogaster	RepARK CLC	1462.63	57.80	101	9,519,212	53,956,504
	RepARK Velvet	1537.49	55.53	101	9,519,228	54,155,904
	REPdenovo	4643.07	44.52	1211	13,194,748	42,044,664
	RepAHR	4735.17	125.72	868	9,530,504	60,185,232
Saccharomyces cerevisiae	RepARK CLC	792.39	25.27	101	4,875,512	29,969,488
	RepARK Velvet	943.62	27.16	100	4,875,512	29,878,280
	REPdenovo	11,229.97	5803.70	316	59,960,388	74,127,816
	RepAHR	2507.21	102.31	856	4,876,644	34,047,800
Acromyrmex echinatior	RepARK CLC	3437.92	154.23	96	18,693,376	86,491,600
	RepARK Velvet	3929.52	194.82	100	18,693,376	86,459,800
	REPdenovo	17,487.81	112.37	1272	25,530,952	77,131,304
	RepAHR	20,763.21	288.73	1554	18,694,492	97,486,232
\(Homo \ sapiens\) chr14	RepARK CLC	1224.70	48.64	102	4,875,512	43,523,184
	RepARK Velvet	1341.06	42.27	101	4,875,532	43,620,064
	REPdenovo	5482.66	40.12	1280	5,853,720	37,027,688
	RepAHR	4273.05	173.32	771	26,354,272	47,734,280
\(Mus\ musculus\)	RepARK CLC	9245.10	709.18	101	36,635,684	329,177,184
	RepARK Velvet	8977.43	421.34	100	36,635,676	333,214,224
	REPdenovo	52,429.50	1047.07	1178	133,069,768	312,131,728
	RepAHR	633,171.42	8987.20	2701	257,398,252	598,113,592

\('User \, Time (s)'\) indicates the process spent in user mode. \('System \, Time (s)'\) indicates the process spent in system mode. \('Percent\,of\,CPU\,this\,job\,got'\) represents the percentage of the job using CPU. \('Maximum\, resident\, set\, size'\) represents the maximum resident memory size of the job. \('File\, system\, outputs'\) indicates the number of files output by this job

ISSN: 1471-2105