Table 3. Runtime of ContextMap 2 and KLEAT.
| Data set | Rep. | Method | CPU time (h) |
|---|---|---|---|
| A549 | 1 | Trans-ABySS | 116.63 |
| KLEAT | 196.28 | ||
| ContextMap | 87.55 | ||
| A549 | 2 | Trans-ABySS | 128.87 |
| KLEAT | 193.73 | ||
| ContextMap | 111.23 | ||
| MCF-7 | 1 | Trans-ABySS | 164.77 |
| KLEAT | 297.22 | ||
| ContextMap | 133.75 | ||
| MCF-7 | 2 | Trans-ABySS | 162.47 |
| KLEAT | 259.57 | ||
| ContextMap | 133.63 | ||
| H1-hESC | 1 | Trans-ABySS | 167.87 |
| KLEAT | 438.57 | ||
| ContextMap | 92.93 | ||
| H1-hESC | 2 | Trans-ABySS | 140.82 |
| KLEAT | 182.87 | ||
| ContextMap | 99.82 |
Runtime of Trans-ABySS using k-mer lengths of 32, 52 and 72, KLEAT applied to the Trans-ABySS output, and ContextMap 2 using default parameters was obtained using 8 cores on the same machines and measured using the Unix “time” command. CPU time was calculated as the sum of “usr” and “sys” time.