Table 2 kmer counting time, dissimilarity calculation time, and total time as well as memory usage used by Cafe and Afann to calculate the pairwise \(d_{2}^{s}, d_{2}^{*}\), and CVTree using K=12 and M=10 among a dataset of 92 white oak NGS samples of 300 Mbp
Counting (min) | Calculation (min) | Total time (min) | Memory (Mb) | |
|---|---|---|---|---|
Cafe-\(d_{2}^{s}\) | 450.2 | 4260.2 | 4710.4 | 1916 |
Afann-\(d_{2}^{s}\) | 21.9 | 31.2 | 53.1 | 449 |
Cafe-\(d_{2}^{*}\) | 450.2 | 4224.1 | 4764.3 | 1928 |
Afann-\(d_{2}^{*}\) | 21.9 | 14.2 | 36.1 | 304 |
Afann-\(d_{2}^{*}\)-fast | 21.9 | 0.3 | 22.2 | 11953 |
Cafe-CVTree | 450.2 | 4295.4 | 4745.6 | 1960 |
Afann-CVTree | 21.9 | 14.1 | 36.0 | 304 |
Afann-CVTree-fast | 21.9 | 0.3 | 22.2 | 11953 |
Mash min | 21.5 | 0.1 | 21.5 | 3 |
Mash opt | 125.6 | 25.5 | 151.1 | 20830 |
Skmer min | NA | NA | 111.9 | 565 |
Skmer opt | NA | NA | 656.9 | 2556 |