Table 2.
Reads alignment softwares.
| NAME | AVERAGE ALIGNMENTS SPEED (MILLION READS/CPU HOUR) | MAXIMUM SENSITIVITY (%) | ALLOWED GAPPED | REFERENCES |
|---|---|---|---|---|
| Bowtie | ∼2.3 | 96.52 | No | 45,56,60 |
| BWA | ~3 | 94.40 | Yes | 45,56,60 |
| CUSHAW | >30 (GPU) | 96.73 | No | 56,60 |
| GEM | >9 | 95.26 | Yes | 56,60 |
| Soap | ∼3 | 98.12 | Yes | 45,56,60 |
| GSNAP | 1.8∼2.8 | 94 | Yes | 49,199 |
| Tophat/Tophat2 | 5∼10 | 96.1 | Yes | 50,199 |
Notes: In general, the sensitivity and speed are in inverse correlation. The benchmark tests of the following tools have been conducted by different studies under specific conditions; therefore, caution is needed when comparing them with each other.