Table 2. Evaluation on real data.
| Default Settings | Loose Settings | |||||
| Program | Hours | % | Conf (%) | Hours | % | Conf (%) |
| BWA-WES1 | 3.350 | - | 97.31 | 7.130 | - | 97.39 |
| CGAP-align-WES1 | 2.887 | 86.18 | 97.31 | 6.375 | 89.41 | 97.39 |
| CGAP-align*-WES1 | 2.698 | 80.54 | 97.31 | 3.813 | 53.48 | 97.33 |
| Bowtie2-WES1 | 3.117 | 93.04 | 98.43 | - | - | - |
| SOAPv2-WES1 | 1.076 | 32.12 | 93.85 | - | - | - |
| BWA-WES2 | 4.555 | - | 96.84 | 11.158 | - | 96.92 |
| CGAP-align-WES2 | 3.857 | 84.68 | 96.84 | 9.699 | 86.92 | 96.92 |
| CGAP-align*-WES2 | 3.829 | 84.06 | 96.84 | 5.598 | 50.17 | 96.85 |
| Bowtie2-WES2 | 3.700 | 81.23 | 98.02 | - | - | - |
| SOAPv2-WES2 | 1.314 | 28.85 | 92.94 | - | - | - |
| BWA-WGS1 | 22.818 | - | 91.84 | 71.349 | - | 92.26 |
| CGAP-align-WGS1 | 20.817 | 91.23 | 91.84 | 66.262 | 92.87 | 92.26 |
| CGAP-align*-WGS1 | 19.717 | 86.41 | 91.84 | 30.159 | 42.27 | 92.19 |
| Bowtie2-WGS1 | 8.433 | 36.96 | 83.31 | - | - | - |
| SOAPv2-WGS1 | 10.311 | 45.19 | 82.03 | - | - | - |
| BWA-WGS2 | 8.504 | - | 93.69 | 20.244 | - | 93.82 |
| CGAP-align-WGS2 | 7.629 | 89.71 | 93.69 | 19.218 | 94.93 | 93.82 |
| CGAP-align*-WGS2 | 7.047 | 82.87 | 93.69 | 9.379 | 46.33 | 93.76 |
| Bowtie2-WGS1 | 5.283 | 61.12 | 84.45 | - | - | - |
| SOAPv2-WGS2 | 4.647 | 54.64 | 88.34 | - | - | - |
29.2 million read pairs (WES1), 31.6 million read pairs (WES2), 107.8 million read pairs (WGS1) and 86.3 million read pairs (WGS2) were mapped to the human genome. The run time (BWA in hours, CGAP-align and SOAP in percentage relative to BWA) on a 2.4 GHz Dual-Core AMD Opteron Processor 2216 HE with 4 threads running simultaneously (Hours & percentage relative to BWA), percent of confidently mapped reads including paired mapping (Conf) are shown.