Table 1 Comparison of the construction performance with the construction time and memory for all datasets
Dataset | n | Method | CONSTRUCT | INDEX | CONSTRUCT |
|---|---|---|---|---|---|
MEMORY | SIZE | TIME | |||
SARS-25k | 751,526,774 | RLCSA | 9.90 | 0.026 | 322.85 |
RLFM | 3.47 | 0.136 | 363.74 | ||
FIGISS | 4.89 | 0.003 | 378.49 | ||
PFP-FM | 12.99 | 4.318 | 117.29 | ||
PFP-FM-CSA | 15.68 | 1.689 | 772.98 | ||
FM-index | 13.35 | 4.399 | 120.08 | ||
Bowtie | 3.55 | 0.47 | 7851.35 | ||
Bowtie2 | 3.54 | 0.59 | 6847.03 | ||
SARS-50k | 1,503,252,577 | RLCSA | 19.88 | 0.051 | 679.89 |
RLFM | 6.94 | 0.278 | 701.36 | ||
FIGISS | 12.44 | 0.006 | 795.70 | ||
PFP-FM | 26.12 | 8.763 | 233.04 | ||
PFP-FM-CSA | 30.95 | 3.078 | 1546.75 | ||
FM-index | 26.12 | 8.490 | 237.50 | ||
Bowtie | 7.09 | 0.94 | 28238.74 | ||
Bowtie2 | 7.09 | 1.18 | 15242.00 | ||
SARS-100k | 3,004,588,730 | RLCSA | 39.47 | 0.099 | 1690.22 |
RLFM | 25.01 | 0.571 | 1432.16 | ||
FIGISS | 25.57 | 0.009 | 1840.80 | ||
PFP-FM | 53.90 | 18.156 | 489.45 | ||
PFP-FM-CSA | 61.86 | 5.758 | 3150.72 | ||
FM-index | 51.85 | 16.73 | 434.55 | ||
Bowtie | 14.20 | 1.884 | 32143.48 | ||
Bowtie2 | 14.19 | 2.37 | 33914.46 | ||
GRCh38 | 3,189,750,467 | RLCSA | 45.45 | 2.022 | 924.60 |
RLFM | 26.31 | 3.101 | 1839.25 | ||
FIGISS | 34.65 | 1.538 | 1440.19 | ||
PFP-FM | 71.13 | 37.862 | 1154.12 | ||
FM-index | 70.93 | 32.54 | 877.43 | ||
PFP-FM-CSA | N/A | N/A | N/A | ||
Bowtie | 13.99 | 1.833 | 2160.76 | ||
Bowtie2 | 14.00 | 2.31 | 2170.32 |