Table 2.
Total run time 4-core 2 GHz Intel Xeon CPU on full genomes [panel (a)] and memory usage in gigabytes on the same genomes [panel (b)]
| Reference | Size | Query | Size | L | MUMmer | vmatch | K = 1 | K = 2 | K = 3 | K = 4 |
|---|---|---|---|---|---|---|---|---|---|---|
| Panel (a) Run time | ||||||||||
| Drosophila simulans | 139 Mbp | D.sechellia | 168 Mbp | 50 | 10m1s | 9m2s | 8m0s | 6m39s | 8m37s | 17m40s |
| Drosophila melanogaster | 170 Mbp | D.sechellia | 168 Mbp | 50 | 9m32s | 10m8s | 9m56s | 8m14s | 12m27s | 23m14 |
| Drosophila melanogaster | 170 Mbp | D.yakuba | 167 Mbp | 50 | 13m11s | 11m56s | 9m26s | 8m29s | 12m45s | 28m15s |
| Mouse | 2.6 Gbp | Human | 3.1 Gbp | 100 | F | F | F | F | 3h46m51s | 9h1m38s |
| Human | 3.1 Gbp | Chimp | 3.4 Gbp | 100 | F | F | F | F | 3h15m3s | 6h41m36s |
| Panel (b) Memory usage in gigabytes | ||||||||||
| Drosophila simulans | 139 Mbp | D.sechellia | 168 Mbp | 50 | 2.19 | 1.30 | 1.44 | 0.79 | 0.57 | 0.47 |
| Drosophila melanogaster | 170 Mbp | D.sechellia | 168 Mbp | 50 | 2.68 | 1.59 | 1.77 | 0.97 | 0.69 | 0.56 |
| Drosophila melanogaster | 170 Mbp | D.yakuba | 167 Mbp | 50 | 2.68 | 1.60 | 1.81 | 0.98 | 0.70 | 0.57 |
| Mouse | 2.6 Gbp | Human | 3.1 Gbp | 100 | F | F | F | F | 11.09 | 9.10 |
| Human | 3.1 Gbp | Chimp | 3.4 Gbp | 100 | F | F | F | F | 12.97 | 10.47 |
F designates the program failed to run on the inputs. h, m, s designate hours, minutes and seconds, respectively. Mbp denotes million base pairs and Gbp denotes billion base pairs. K = 2,3,4, use 2, 3 and 4 cores, respectively.