Table 4 Simulated single-end reads: search time and percent of correct alignments
From: A random-permutations-based approach to fast read alignment
Read length | 75 | 100 | 150 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
Mismatch probability | 1% | 2% | 5% | 1% | 2% | 5% | 1% | 2% | 5% | |
Software | Time/%Correct | Â | Â | Â | Â | Â | Â | Â | Â | Â |
Bowtie -v 3 | time (s) % correct | 141 94.9 | 245 89.0 | 517 45.0 | 177 94.4 | 350 81.9 | 588 24.1 | 306 89.5 | 537 60.9 | 647 5.0 |
Bowtie -v 2 | time (s) % correct | 58 91.1 | 90 76.2 | 165 25.1 | 79 87.6 | 125 63.7 | 190 11.0 | 126 76.2 | 194 38.9 | 218 1.6 |
Bowtie -n 3 | time (s) % correct | 152 92.6 | 236 84.6 | 439 67.7 | 234 92.5 | 393 78.8 | 961 65.2 | 397 88.2 | 733 59.4 | 2430 41.9 |
Bowtie -n 2 | time (s) % correct | 108 93.1 | 161 85.7 | 286 69.6 | 170 93.0 | 264 79.7 | 609 67.0 | 294 88.6 | 514 59.9 | 1560 43.1 |
Bowtie -n 2 -k 10 | time (s) % correct | 873 96.2 | 869 88.7 | 1179 72.9 | 1242 95.3 | 1069 81.7 | 2377 69.2 | 1511 90.3 | 1243 61.0 | 3446 44.0 |
Bowtie2 -very-fast | time (s) % correct | 169 93.6 | 163 87.3 | 136 59.5 | 234 95.3 | 233 91.2 | 196 69.4 | 363 95.9 | 366 93.0 | 299 76.1 |
Bowtie2 -fast | time (s) % correct | 224 94.0 | 223 88.2 | 178 60.8 | 329 95.9 | 320 92.4 | 267 71.0 | 533 96.9 | 523 94.7 | 422 78.2 |
Bowtie2 -sensitive | time (s) % correct | 354 95.2 | 315 92.1 | 275 73.1 | 498 96.5 | 462 94.6 | 396 80.4 | 791 97.6 | 765 96.6 | 638 88.4 |
Bowtie2 -very sensitive | time (s) % correct | 776 95.7 | 734 94.2 | 611 83.6 | 1124 96.8 | 1056 95.8 | 851 89.1 | 1864 97.8 | 1730 97.3 | 1383 94.2 |
Bowtie2 -very sensitive -k 10 | time (s) % correct | 1063 98.0 | 813 95.8 | 691 84.6 | 1743 98.4 | 1341 96.6 | 1165 89.9 | 3498 98.9 | 2775 97.6 | 2395 94.9 |
BWA -o 0 | time (s) % correct | 320 96.5 | 457 93.3 | 516 59.9 | 404 97.2 | 743 93.9 | 610 54.2 | 715 97.4 | 931 92.5 | 447 33.1 |
BWA -o 1 | time (s) % correct | 359 97.1 | 560 93.8 | 889 60.2 | 483 98.1 | 1007 94.7 | 1206 54.6 | 904 98.7 | 1513 93.6 | 1034 33.4 |
Permutations-based (mode 1) | time (s) % correct | 53 97.5 | 76 95.8 | 106 84.5 | 56 98.4 | 90 97.5 | 118 89.0 | 76 98.5 | 98 98.0 | 112 91.3 |
Permutations-based (mode 2) | time (s) % correct | 147 97.8 | 149 96.4 | 152 86.6 | 155 98.5 | 147 97.8 | 145 90.6 | 145 98.6 | 148 98.1 | 156 92.7 |
Permutations-based (fast) | time (s) % correct | 31 93.7 | 43 88.5 | 62 64.1 | 33 95.8 | 46 91.5 | 64 66.9 | 45 96.9 | 51 93.3 | 72 69.4 |