Table 3 Pairwise correlations of distance matrices on “E. coli” dataset. The last two columns show the runtime on the “E. coli” dataset. Assembly time (without distance matrix calculation) on the same dataset is \(24{,}980\,\textrm{s}\) (ABySS), \(17{,}514\,\textrm{s}\) (Edena), \(1021{,}184\,\textrm{s}\) (SPAdes), \(229{,}350\,\textrm{s}\) (SSAKE), and \(17{,}608\,\textrm{s}\) (Velvet). See the Supplementary materials for results of all tested methods
\(\mathsf{Method}\) | \(\mathsf{dist}_{\mathsf{MESSGMq}\alpha }\) | \(\mathsf {co-phylog}\) | \(\mathsf{Mash}\) | \(D_{2}\) | \(D_{2}^{*}\) | \(D_{2}^{q}\) | \(D_{2}^{q*}\) | \(\mathsf{dist}_{q}\) Velvet | \(\mathsf{Time}\) (\(\textrm{s},\ \mathsf{one thread}\)) | \(\mathsf{Time}\ (\textrm{s},\ \mathsf{parallel})\) |
|---|---|---|---|---|---|---|---|---|---|---|
\(\mathsf{dist}_{\mathsf{MESSGMq}\alpha }\) | 1.000 | 0.831 | 0.943 | 0.683 | 0.867 | 0.684 | 0.868 | 1.000 | 8,908 | NaN |
\(\mathsf {co-phylog}\) | 0.831 | 1.000 | 0.925 | 0.711 | 0.813 | 0.712 | 0.813 | 0.829 | NaN | 598 |
\(\mathsf{Mash}\) | 0.943 | 0.925 | 1.000 | 0.734 | 0.877 | 0.735 | 0.878 | 0.942 | NaN | 500 |
\(D_{2}\) | 0.683 | 0.711 | 0.734 | 1.000 | 0.949 | 1.000 | 0.949 | 0.683 | 3,289 | NaN |
\(D_{2}^{*}\) | 0.867 | 0.813 | 0.877 | 0.949 | 1.000 | 0.950 | 1.000 | 0.866 | 3,329 | NaN |
\(D_{2}^{q}\) | 0.684 | 0.712 | 0.735 | 1.000 | 0.950 | 1.000 | 0.949 | 0.684 | 3,302 | NaN |
\(D_{2}^{q*}\) | 0.868 | 0.813 | 0.878 | 0.949 | 1.000 | 0.949 | 1.000 | 0.868 | 3,329 | NaN |
\(\mathsf{dist}_{q}\) Velvet | 1.000 | 0.829 | 0.942 | 0.683 | 0.866 | 0.684 | 0.868 | 1.000 | 88,156 | 4,276 |