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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
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
  1. 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