Table 1.
Runtime and memory benchmark results
| Read length | Algorithm | Runtime (s) |
Memory (GB) | ||
|---|---|---|---|---|---|
| SIM1 | SIM2 | SIM3 | |||
| 50 | RASER | 592.6 | 587.28 | 618.9 | 10.8 |
| RASER DF | 625.07 | 617.85 | 639.6 | 10.8 | |
| RASER OB | 706.51 | 698.05 | 721.27 | 10.8 | |
| GSNAP | 1869.37 | 1657.21 | 3310.93 | 24.8 | |
| STAR | 9 | 11 | 10 | 28.9 | |
| TOPHAT2 | 636 | 618 | 638 | 4.3 | |
| 100 | RASER | 724.93 | 748.41 | 768.43 | 10.8 |
| RASER DF | 854.06 | 899.75 | 919.89 | 10.8 | |
| RASER OB | 951.95 | 1013.68 | 1021.67 | 10.8 | |
| GSNAP | 549.58 | 366.21 | 482.04 | 24.8 | |
| STAR | 11 | 13 | 15 | 28.9 | |
| TOPHAT2 | 814 | 858 | 921 | 4.8 | |
| 150 | RASER | 1143.79 | 1241.51 | 1262.79 | 10.8 |
| RASER DF | 1502.06 | 1641.47 | 1557.84 | 10.8 | |
| RASER OB | 1644.49 | 1800.12 | 1687.85 | 10.8 | |
| GSNAP | 1015.73 | 848.68 | 1294.81 | 24.8 | |
| STAR | 23 | 25 | 32 | 28.9 | |
| TOPHAT2 | 1085 | 1189 | 1252 | 5.3 | |
| 200 | RASER | 1682.08 | 1789.76 | 1812.85 | 10.8 |
| RASER DF | 2278.6 | 2341.39 | 2411.74 | 10.8 | |
| RASER OB | 2542.26 | 2580.5 | 2657.54 | 10.8 | |
| GSNAP | 849.71 | 867.47 | 1773.6 | 24.8 | |
| STAR | 25 | 31 | 42 | 28.9 | |
| TOPHAT2 | 1361 | 1508 | 1651 | 5.9 | |
Comparison performed using 1 M reads, eight threads for each algorithm. There was no difference in memory usage for different sets of simulated datasets. RASER DF, RASER with double filtering; RASER OB, RASER with obviously best mapping.