Table 3.
Comparison of 6 read-mapping tools on the E. coli 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 | 456,416 (45.64%) | 423,541 (42.35%) | 0m18s |
| BWA | 456,928 (45.69%) | 424,239 (42.42%) | 0m21s |
| MAQ | 646,523 (64.65%) | 588,362 (58.84%) | 1m08s |
| PerM | 413,102 (41.31%) | 384,050 (38.40%) | 0m23s |
| SHRiMP 1.3.2 | 687,855 (68.79%) | — | 3m33s |
| SHRiMP 2.0 | 714,662 (71.47%) | — | 0m41s |
| STORM | 773,155 (77.32%) | 697,164 (69.72%) | 0m57s |