Table 1.
Metrics for simulated Nanopore read mapping to the human genome.a
| Minimap2 |
MashMap2 |
MashMap3 |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Dataset | CPU time (m) | Memory (GB) | ME | MAE | CPU time (m) | Memory (GB) | ME | MAE | CPU time (m) | Memory (GB) | ME | MAE |
| CLR-99 | 154.20 | 9.89 | −0.25 | 0.34 | 80.27 | 9.92 | −0.27 | 0.29 | 33.64 | 13.07 | 0.03 | 0.17 |
| CLR-98 | 147.29 | 9.89 | −0.36 | 0.52 | 82.46 | 9.92 | −0.33 | 0.39 | 35.13 | 13.09 | 0.06 | 0.29 |
| CLR-95 | 96.35 | 9.89 | −0.46 | 0.81 | 106.81 | 9.92 | −0.25 | 0.59 | 42.81 | 13.10 | 0.21 | 0.62 |
a
Minmer and minimizer-based MashMap implementations as well as Minimap2 were used to map simulated reads from the human reference genome using Pbsim (Ono et al. 2013) and the mean error and mean absolute error are reported. Bolded values signify the best performance for each dataset.