Aligner | Execution time (Hrs) | % reads mapped uniquely |
---|
BLAT
| 84.5 | 94.1 |
BWA-SW
| 1.8 | 89.8 |
Pash high
| 5.4 | 96.2 |
Pash med
| 3.0 | 95.9 |
Pash low
| 2.4 | 95.7 |
Pash 3.0 fast
| 1.8 | 96.1 |
SSAHA2
| 14.3 | 96.9 |
- Execution time, in hours, and percent of reads uniquely mapped with at least 90% identity. Pash 3.0 is run with four different sensitivity settings: high, medium, low, and fast. SSAHA2 is run with the -454 flag, and BLAT is run with default parameters (tile size 11, requiring 2 seeds for a match). Pash is 2.6 to 7.9 times faster than SSAHA, with a sensitivity loss of 0.7-1.2%. Pash is 15-47 times faster than BLAT.