Table 2.
Comparison of 6 read-mapping tools on S. cerevisiae dataset. The execution time refers to all steps, including index construction for the tools that can reuse the result of this step (Bowtie, BWA, MAQ).
| Program | Mapped reads | Unique mapping positions | Execution time |
|---|---|---|---|
| Bowtie | 553,140 (43.20%) | 512,086 (39.99%) | 0m50s |
| BWA | 422,550 (33.00%) | 395,342 (30.87%) | 0m38s |
| MAQ | 616,497 (48.14%) | 567,549 (44.32%) | 1m20s |
| PerM | 418,524 (32.68%) | 347,668 (27.15%) | 0m31s |
| SHRiMP 1.3.2 | 663,923 (51.85%) | — | 7m56s |
| SHRiMP 2.0 | 709,146 (55.38%) | — | 1m22s |
| STORM | 839,633 (65.57%) | 754,402 (58.91%) | 2m10s |