Table 8.
Classification performance
| Simulated |
Real |
||||||
|---|---|---|---|---|---|---|---|
| Reference | Method | Mbp/m | Wall time | Memory | Mbp/m | Wall time | Memory |
| RefSeq-CG-top-3 | Centrifuge | 298 | 00:24:59 (±51 s) | 13 | 802 | 00:09:19 (±4 s) | 13 |
| Clark | 1104 | 00:06:44 (±5 s) | 101 | 1208 | 00:06:11 (±4 s) | 100 | |
| Diamond | 36 | 03:27:00 (±259 s) | 14 | 33 | 03:40:55 (±170 s) | 15 | |
| Ganon | 380 | 00:20:31 (±8 s) | 61 | 538 | 00:14:50 (±1 s) | 61 | |
| Kraken | 2113 | 00:03:46 (±1 s) | 177 | 2734 | 00:02:57 (±3 s) | 177 | |
| Kraken2 | 3085 | 00:02:47 (±1 s) | 27 | 3833 | 00:02:19 (±1 s) | 27 | |
| RefSeq-ALL-top-3 | Diamond | 6 | 18:23:09 (±729 s) | 21 | 5 | 21:23:00 (±181 s) | 22 |
| Ganon | 107 | 01:13:44 (±7s) | 243 | 153 | 00:53:13 (±12 s) | 243 | |
| Kraken2 | 2991 | 00:04:11 (±4s) | 123 | 3659 | 00:03:52 (±1 s) | 122 | |
Note: Memory in GiB. Full set of simulated and real reads classified with 48 threads. Centrifuge, clark and diamond performance in Mbp/m calculated from wall time. Values are the average of four out five consecutive runs (excluding the slowest run), with SD for the run-time in parentheses. Computer specifications and parameters used are in the Supplementary Sections S2.1 and S2.4.