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 |