Table 3 The performance evaluation on HG38 and the diploid sequence of NA12878. The performance on SNV and Indel detection implies that the diploid genome sequence and the reference variants are not fully compatible
From: GSAlign: an efficient sequence alignment tool for intra-species genomes
Dataset | Method | SNV | Indel | Run time (min) | Memory usage (GB) | ||
|---|---|---|---|---|---|---|---|
Precision | Recall | Precision | Recall | ||||
NA12878 (Diploid) | GSAlign | 0.832 | 0.969 | 0.759 | 0.767 | 5 | 14 |
Minimap2 | 0.830 | 0.970 | 0.754 | 0.768 | 65 | 23 | |
MUMmer4 | 0.752 | 0.946 | 0.711 | 0.749 | 3898 | 57 | |
LAST | 0.832 | 0.969 | 0.760 | 0.764 | 1305 | 28 | |