Table 4.
Performance comparison for large read sets
| Read Count | Aligner | Effective Time (HMS) | Aligns/min |
|---|---|---|---|
| 1 000 000 | PALADIN | 00:07:10 | 139 535 |
| 1 000 000 | RAPSearch2 | 32:54:59 | 506 |
| 1 000 000 | DIAMOND | 00:51:42 | 19 342 |
| 1 000 000 | Lambda | 04:46:23 | 3492 |
| 240 000 000 | PALADIN | 31:15:02 | 127 998 |
| 240 000 000 | BLASTX | 250 000:00:00 | 16 |
Performance evaluation of the three applicable BLAST competitors was performed against a 1 000 000 read subset of the full 240 000 000 read set. To estimate the linear portion of alignments per second, the effective time reflects the difference between total time and the constant setup time of loading the indexed reference. Due to obvious time constraints in the case of the BLASTX comparison, alignment rate was calculated using an 8000 read subset, from which the effective time was estimated. For this final test, the PALADIN was given the entire 240 000 000 set as a query. In both tests, PALADIN outperformed all other alignment tools.