Gerbil: a fast and memory-efficient k-mer counter with GPU-support

Erbert, Marius; Rechner, Steffen; Müller-Hannemann, Matthias

doi:10.1186/s13015-017-0097-9

Algorithms for Molecular Biology

Table 3 Running times in the format mm:ss (the best performing in italics)

From: Gerbil: a fast and memory-efficient k-mer counter with GPU-support

Data set	k	System one				System two
Data set	k	Gerbil	gGerbil	KMC2	DSK	Gerbil	gGerbil	KMC2	DSK
F. vesca	28	02:15	01:47	01:51	02:53	01:37	01:21	01:32	02:05
	40	02:23	01:58	02:49	04:13	01:49	01:31	02:12	02:52
	56	02:31	01:59	03:05	03:52	01:53	01:31	02:30	02:50
	65	03:02	02:12	04:23	05:23	02:05	01:42	03:35	03:37
M. balbisiana	28	14:48	12:04	12:24	13:50	11:37	10:09	10:50	11:06
	40	13:55	12:41	15:50	15:30	11:35	10:30	13:46	12:26
	56	12:40	11:31	15:43	14:30	10:51	09:55	13:36	11:44
	65	12:58	11:38	18:48	16:52	10:55	09:57	15:47	12:34
G. gallus	28	21:10	15:07	15:26	25:44	16:14	12:50	13:10	21:00
	40	20:30	16:23	19:22	31:19	16:09	13:15	16:49	23:48
	56	18:58	15:32	19:19	24:04	15:16	12:54	16:48	19:59
	65	20:12	15:50	22:27	26:04	15:48	13:22	19:25	21:33
H. sapiens	28	46:41	32:04	31:24	66:16	33:54	25:18	26:44	50:15
	40	50:14	37:59	44:06	102:48	34:30	26:40	35:59	54:21
	56	44:05	34:21	43:56	60:29	34:30	26:40	35:25	45:32
	65	43:32	35:46	53:31	96:31	32:01	26:21	42:19	47:50
H. sapiens 2	28	73:29	53:55	50:09	146:10	54:19	39:05	41:47	76:50
	40	77:54	62:12	71:27	209:12	53:31	42:27	57:02	83:59
	56	67:28	57:22	70:46	138:06	50:25	40:18	56:28	72:35
	65	68:50	58:41	87:14	156:05	50:53	42:28	68:10	78:13
GRCh38	28	62:19	50:19	43:46	65:20	34:52	18:49	21:36	25:23
	40	69:00	61:03	68:47	116:08	36:52	24:32	39:57	40:54
	56	78:44	70:57	80:40	111:39	37:10	26:15	48:59	41:13
	65	80:43	73:27	114:00	225:35	42:54	33:08	79:34	73:25
	100	82:30	81:35	178:04	ME	45:34	38:43	136:20	114:09
	125	79:55	77:42	226:02	ME	44:41	40:09	174:28	133:56
	150	83:04	82:33	293:02	NS	49:03	45:23	TL	NS
	175	86:07	85:51	TL	NS	53:14	50:35	TL	NS
	200	93:48	90:49	TL	NS	60:03	56:25	TL	NS
N. crassa	28	20:29	09:55	09:49	25:41	10:47	07:31	06:45	17:31
	40	22:15	11:50	15:45	34:31	12:15	09:21	11:32	23:52
	56	23:16	12:01	18:15	32:03	12:24	09:14	13:36	22:33
	65	27:13	16:00	27:34	44:19	15:19	11:13	21:06	31:07
	80	26:26	17:16	31:46	41:22	15:17	11:25	23:47	29:27
	100	28:18	21:09	TL	74:57	17:39	13:28	36:45	37:05
	125	28:56	22:37	TL	76:06	17:43	13:53	47:41	36:42
	150	30:44	26:18	TL	NS	18:49	15:30	TL	NS
	175	33:04	29:01	TL	NS	20:26	17:43	TL	NS
	200	37:05	34:33	TL	NS	21:48	19:51	TL	NS
A. thaliana	28	33:53	19:09	19:41	43:00	22:38	16:14	15:00	32:48
	40	42:41	25:24	28:27	55:14	26:30	19:14	22:11	40:27
	56	43:59	27:53	33:48	52:06	26:52	19:36	25:29	39:07
	65	48:22	34:05	TL	114:34	30:07	23:05	38:33	55:01
	80	48:24	38:32	TL	109:43	30:42	23:25	43:06	54:06
	100	51:01	42:37	TL	141:28	33:18	27:29	67:09	73:30
	125	52:17	44:49	DS	148:44	33:31	28:11	TL	79:14
	150	53:47	49:00	TL	NS	35:26	39:17	TL	NS
	175	58:55	53:37	TL	NS	38:07	35:37	TL	NS
	200	66:42	62:31	TL	NS	40:17	39:31	TL	NS

Some runs were aborted after a time limit of 5 h (TL). In addition, some runs failed due to insufficient disk space (DS) or memory errors (ME). In addition, DSK simply does not support values of k > 127 (NS). The label ‘gGerbil’ stands for Gerbil with activated GPU mode. Instead, standard ‘Gerbil’ does not use any GPU

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ISSN: 1748-7188

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