Table 2.
Comparison of computational speeds for a subset of annotations between the current and previous version of SNPnexus. Ensembl, RefSeq and COSMIC annotations are the most computationally intensive. Using an input file of 100k variants, SNPnexus now operates 16×, 15.5× and 82× faster than its predecessor for these annotations, respectively. SIFT is included to show that even for non-intensive annotations there is a noticeable improvement
| Processing time (s) | |||
|---|---|---|---|
| Annotation | Number of variants | SNPnexus v.3 | SNPnexus v.4 |
| Ensembl | 5k | 172 | 7.36 |
| 20k | 2170 | 65.75 | |
| 50k | 3909 | 158.19 | |
| 100k | 7941 | 486.69 | |
| RefSeq | 5k | 137 | 4.28 |
| 20k | 1405 | 35.82 | |
| 50k | 4265 | 347.31 | |
| 100k | 7283 | 469.7 | |
| SIFT | 5k | 15 | 0.63 |
| 20k | 28 | 2.96 | |
| 50k | 49 | 39.67 | |
| 100k | 59 | 46.06 | |
| COSMIC | 5k | 2632 | 2.4 |
| 20k | 4623 | 10.46 | |
| 50k | 8706 | 114.51 | |
| 100k | 14279 | 173.53 | |