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| Program | Runtime (s) | Speedup factor |
|---|---|---|
| BatAlign - Default | 583 | 1.2 |
| BatAlign - Faster | 481 | 1.4 |
| BatAlign - Fastest | 331 | 2.0 |
| Bowtie2 | 459 | 1.5 |
| BWA-Short | 598 | 1.1 |
| BWA-SW | 639 | 1.1 |
| GEM | 214 | 3.2 |
| SeqAlto | 677 | 1.0 |
| BWA-MEM | 219 | 3.1 |
Fastest speed up in bold.
