Table 2 The performance evaluation on the three GRCh38 synthetic data sets. The indexing time of each method is not included in the run time. They are 110 (BWT-GSAlign), 129 (Suffix array-MUMmer4), and 2.6 min (Minimizer-Minimap2), respectively
From: GSAlign: an efficient sequence alignment tool for intra-species genomes
Dataset | Method | SNV | Indel | Local align# | Run time (min) | ||
|---|---|---|---|---|---|---|---|
precision | recall | precision | recall | ||||
SimHG-1X | GSAlign | 1.000 | 1.000 | 0.999 | 0.999 | 250 | 11 |
Minimap2 | 1.000 | 0.996 | 0.999 | 0.995 | 417 | 39 | |
MUMmer4 | 0.998 | 0.932 | 0.985 | 0.932 | 3111 | 869 | |
LAST | 1.000 | 0.992 | 0.992 | 0.947 | 1168 | 2524 | |
SimHG-3X | GSAlign | 1.000 | 0.998 | 0.994 | 0.997 | 366 | 18 |
Minimap2 | 1.000 | 0.996 | 0.991 | 0.995 | 561 | 37 | |
MUMmer4 | 0.989 | 0.923 | 0.796 | 0.925 | 4925 | 289 | |
LAST | 1.000 | 0.990 | 0.809 | 0.950 | 1234 | 1185 | |
SimHG-5X | GSAlign | 1.000 | 0.993 | 0.958 | 0.992 | 587 | 24 |
Minimap2 | 1.000 | 0.995 | 0.952 | 0.994 | 1058 | 40 | |
MUMmer4 | 0.986 | 0.907 | 0.486 | 0.912 | 5513 | 157 | |
LAST | 1.000 | 0.981 | 0.461 | 0.947 | 1636 | 458 | |