Table 3.
Comparison of MaxSSmap and MaxSSmap_fast to a GPU and a SIMD high performance Smith-Waterman implementation
| (a) Percent of 100,000 251 bp reads mapped correctly to the E.coli genome. Shown in parenthesis are incorrectly mapped reads and remaining are rejected | ||||
|---|---|---|---|---|
| Div | MaxSSmap_fast | MaxSSmap | CUDASW++ | SSW |
| Reads without gaps | ||||
| .1 | 95 (0.4) | 96 (0.4) | 94 (0.9) | 97 (3) |
| .2 | 95 (0.6) | 95.3 (0.6) | 94 (1) | 97 (3) |
| .3 | 90 (1.1) | 94.2 (0.9) | 93 (1.3) | 96 (4) |
| Reads with gaps | ||||
| .1 | 92 (1.5) | 93.1 (1.9) | 94 (0.9) | 97 (3) |
| .2 | 90 (1.7) | 92.5 (2.1) | 92 (1) | 96 (4) |
| .3 | 81 (2.8) | 89.9 (3.5) | 92 (1.4) | 95 (5) |
| (b) Time in minutes to map 100,000 251 bp reads to the E.coli genome | ||||
| Div | MaxSSmap_fast | MaxSSmap | CUDASW++ | SSW |
| Reads without gaps | ||||
| .1 | 20 | 28 | 164 | 1288 |
| .2 | 20 | 28 | 164 | 1275 |
| .3 | 20 | 28 | 164 | 1255 |
| Reads with gaps | ||||
| .1 | 20 | 28 | 163 | 1283 |
| .2 | 20 | 28 | 162 | 1266 |
| .3 | 20 | 28 | 162 | 1235 |
These are simulated Illumina reads and contain realistic base qualities generated from Illumina short reads. Each divergence represents the average percent of mismatches in the reads. So 0.1 means 10% mismatches on the average. The gaps are randomly chosen to occur in the read or the genome and are of length at most 30.