Table 6.
Performance comparison on real datasets between drFAST-DP, drFAST-CT, Bowtie, SOCS and PerM on 1 million randomly selected reads from three different sequencing experiments
| Dataset | Mapper | Time (min) | Map locations | Reads mapped (%) |
|---|---|---|---|---|
| NA18507 | drFAST-DP | 114 | 189 276 027 | 36.8 |
| drFAST-CT | 54 | 149 362 540 | 35.6 | |
| Bowtie v = 2 | 21 | 64 092 233 | 27.8 | |
| Bowtie n = 2 | 63 | 202 948 323 | 35.2 | |
| SOCS | 320 | 21 081 941 | 35.3 | |
| Mapreads | 80 | 17 032 680 | 37.3 | |
| PerM | 76 | 10 068 062 | 35.3 | |
| NA10847 | drFAST-DP | 200 | 667 928 813 | 47.1 |
| drFAST-CT | 100 | 512 599 230 | 45.9 | |
| Bowtie v = 2 | 84 | 280 928 112 | 38.0 | |
| Bowtie n = 2 | 91 | 270 996 634 | 36.0 | |
| SOCS | 420 | 53 668 622 | 44.8 | |
| Mapreads | 140 | 39 589 079 | 48.5 | |
| PerM | 100 | 20 699 652 | 44.8 | |
| NA12156 | drFAST-DP | 136 | 491 158 791 | 33.5 |
| drFAST-CT | 91 | 440 317 111 | 32.5 | |
| Bowtie v = 2 | 99 | 329 916 108 | 25.0 | |
| Bowtie n = 2 | 99 | 318 621 596 | 23.7 | |
| SOCS | 400 | 38 246 530 | 31.2 | |
| Mapreads | 110 | 22 182 469 | 35.1 | |
| PerM | 140 | 10 798 496 | 31.2 | |
We set the error threshold to 2 bp for all aligners, except PerM, where we set the threshold to four as per the PerM developers suggested. We then removed the alignments with more than 2 bp mismatches for comparison purposes.