Table 6 Total query time and memory used with Fulgor’s two-pass multi-query optimization compared to “normal” single-pass queries (the same as in Table 5b). Here, we benchmark high-hit workloads using 16 processing threads
From: Fulgor: a fast and compact k-mer index for large-scale matching and color queries
Normal | Two-pass optimization | |||||
|---|---|---|---|---|---|---|
mm:ss | GB | mm:ss | GB | % speedup | %+Mem. | |
EC | 02:10 | 1.68 | 01:24 | 2.78 | 35.38 | 65.48 |
SE-5K | 01:16 | 0.82 | 01:09 | 1.47 | 9.21 | 79.27 |
SE-10K | 02:26 | 2.11 | 02:08 | 3.18 | 12.33 | 50.71 |
SE-50K | 19:15 | 18.53 | 11:25 | 21.12 | 40.69 | 13.98 |
SE-100K | 27:30 | 42.78 | 23:00 | 47.16 | 16.36 | 10.24 |
SE-150K | 42:30 | 70.55 | 35:02 | 77.47 | 17.57 | 9.81 |
GB | 01:10 | 30.02 | 01:09 | 36.47 | 1.43 | 21.49 |