Table 3. Run time per test.
| 500k | 1m | 5m | Full chr19 | |
|---|---|---|---|---|
| CasFinder | 00:00:05 | 00:00:12 | 00:01:50 | 00:06:38 |
| CRISPR-ERA | 00:00:16 | 00:00:31 | 00:01:46 | 00:18:27 |
| mm10db | 00:00:17 | 00:00:49 | 00:01:53 | 00:26:03 |
| CRISPR-DO | 00:00:34 | 00:01:52 | 00:22:37 | 00:32:36 |
| GuideScan | 00:00:52 | 00:02:25 | 00:14:19 | 06:53:07 |
| TUSCAN | 00:00:48 | 00:01:38 | 00:06:10 | # |
| FlashFry | 00:00:54 | 00:01:54 | 00:19:07 | * |
| CT-Finder | 00:01:29 | 00:04:41 | 01:11:12 | * |
| GT-Scan | 00:11:05 | 00:42:24 | 10:16:00 | # |
| Cas-Designer CPU | 00:21:21 | 00:51:12 | 06:00:30 | * |
| Cas-Designer GPU | 00:10:06 | 00:38:57 | 04:40:47 | * |
| CCTop | 00:47:39 | 02:31:00 | 09:57:40 | * |
| CHOPCHOP | 00:00:23 | 00:00:45 | 00:04:00 | # |
| CRISPOR | 00:18:37 | 00:41:22 | 04:48:39 | # |
| WU-CRISPR | 00:04:39 | 00:12:20 | 01:55:57 | ^ |
| PhytoCRISP-Ex | 01:21:13 | 09:59:18 | * | - |
| sgRNAScorer2 | 04:04:06 | 16:23:31 | * | - |
| sgRNAcas9 | 15:11:46 | * | - | - |
| SSC | 00:00:01 | ^ | - | - |
Run time denoted as hh:mm:ss for each tool and dataset size. Some tools exceeded the 72-hour limit (*), or were terminated by the the operating system’s out-of-memory killer (#). Any tool failing a test was not considered for larger input sizes (-). WU-CRISPR failed on ‘full’ due to the tool rejecting inputs containing N, and SSC could not process inputs larger than 500,000 bases in length (^).