Table 1.
Example peak memory usage, disk space usage and wall-clock times when running ntLink scaffolding on draft genomes of various sizes. The disk space usage of the input draft assembly and long reads files are not included in the benchmarksa. See Supplementary Tables 1 and 2 for more information about the data used for these example ntLink runs.
| Species | Approximate genome size (Mbp) | Fold coverage of long reads | Peak memory usage (GB) | Peak disk space usage (GB) | Wall-clock time (min) |
|---|---|---|---|---|---|
| Caenorhabditis elegans | 100 | 93 | 0.9 | 0.9 | 6.5 |
| Oryza sativa | 373 | 62 | 3.4 | 2.8 | 21.4 |
| Solanum lycopersicum | 824 | 72 | 5.4 | 5.6 | 43.4 |
| Homo sapiens | 3,055 | 50 | 20.8 | 25.0 | 136.0 (2h16m) |
a
Default ntLink parameters were used for each example run, except for Solanum lycopersicum, which used k=64, w=250. One round of ntLink, including the gap-filling option, was run with each dataset.