Table 1.
Evaluation on simulated data
| Program | Metrics | 100 bp |
200 bp |
500 bp |
1000 bp |
10 000 bp |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2% | 5% | 10% | 2% | 5% | 10% | 2% | 5% | 10% | 2% | 5% | 10% | 2% | 5% | 10% | ||
| BLAT | CPU sec | 685 | 577 | 559 | 819 | 538 | 486 | 1078 | 699 | 512 | 1315 | 862 | 599 | 2628 | 1742 | 710 |
| Q20% | 68.7 | 25.5 | 3.0 | 92.0 | 52.9 | 7.8 | 97.1 | 86.3 | 21.4 | 97.7 | 96.4 | 39.0 | 98.4 | 99.0 | 94.0 | |
| errAln% | 0.99 | 2.48 | 5.47 | 0.55 | 1.72 | 4.55 | 0.17 | 1.12 | 4.41 | 0.01 | 0.52 | 3.98 | 0.00 | 0.00 | 1.28 | |
| BWA-SW | CPU sec | 165 | 125 | 84 | 222 | 168 | 118 | 249 | 172 | 152 | 234 | 168 | 150 | 158 | 134 | 120 |
| Q20% | 85.1 | 62.2 | 19.8 | 93.8 | 88.7 | 49.7 | 96.1 | 95.5 | 85.1 | 96.9 | 96.5 | 95.0 | 98.4 | 98.5 | 98.1 | |
| errAln% | 0.01 | 0.05 | 0.17 | 0.00 | 0.02 | 0.13 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | |
| SSAHA2 | CPU sec | 4872 | 7962 | 9345 | 1932 | 2236 | 5252 | 3311 | 8213 | 6863 | 1554 | 1583 | 3113 | – | – | – |
| Q20% | 85.5 | 83.8 | 78.2 | 93.4 | 93.1 | 91.9 | 96.6 | 96.5 | 96.1 | 97.7 | 97.6 | 97.4 | – | – | – | |
| errAln% | 0.00 | 0.01 | 0.19 | 0.01 | 0.00 | 0.01 | 0.00 | 0.01 | 0.04 | 0.00 | 0.00 | 0.00 | – | – | – | |
Approximately 10 000 000 bp data of different read lengths and error rates are simulated from the human genome. Twenty percent of errors are indel errors with the indel length drawn from a geometric distribution (density: 0.7·0.3l−1). These simulated reads are aligned back to the human genome with BLAT (option -fastMap), BWA-SW and SSAHA2 (option −454 for 100 and 200 bp reads), respectively. The aligned coordinates are then compared with the simulated coordinates to find alignment errors. In each cell in this table, the three numbers are the CPU seconds on a single-core of an Intel E5420 2.5 GHz CPU, percent alignments with mapping quality greater than or equal to 20 (Q20), and percent wrong alignments out of Q20 alignments. SSAHA2 and BWA-SW report mapping quality; BLAT mapping quality is estimated as 250 times the difference of the best and second best alignment scores divided by the best alignment score (essentially the same calculation as the one for BWA-SW).