Table 2.
Seed finding performance on the 1000 Genomes graphs
| Index | Indexing | Covered | Query | ||
|---|---|---|---|---|---|
| size | time | k-mers | time | ||
| AF>1% | PSI/path-only | 6.3 GB | 28 h | 6 721 M (99.24%) | 4.82 μs/occ |
| PSI/hybrid | 6.3 GB | 28 h | 6 773 M (100%) | 6.20 μs/occ | |
| GCSA2 order-128 | 15 GB | 22 ha | 6 712 M (99.09%) | 6.28 μs/occ | |
| All | PSI/path-only | 64 GB | 56 h | 214 394 M (96.50%) | 8.12 μs/occ |
| PSI/hybrid | 64 GB | 56 h | 222 180 M (100%) | 21.05 μs/occ | |
| GCSA2 order-128 | 34 GB | 30 ha | 13 863 M (6.24%) | 20.03 μs/occ |
a
Excluding time spent on pruning the original graph.