Table 3.
Space versus Accuracy trade-off in Squeakr and deBGR
| System | Dataset | Space | Navigational errors |
|
|---|---|---|---|---|
| (bits/k-mer) | Topological | Abundance | ||
| Squeakr | GSM984609 | 18.9 | 14263577 | 16655318 |
| Squeakr (exact) | 50.8 | 0 | 0 | |
| deBGR | 26.5 | 0 | 0 | |
| Squeakr | GSM981256 | 19.4 | 13591254 | 15864754 |
| Squeakr (exact) | 52.1 | 0 | 0 | |
| deBGR | 27.1 | 0 | 0 | |
| Squeakr | GSM981244 | 30.9 | 10462963 | 12257261 |
| Squeakr (exact) | 79.8 | 0 | 0 | |
| deBGR | 37.0 | 0 | 0 | |
| Squeakr | SRR1284895 | 20.9 | 23272114 | 27200821 |
| Squeakr (exact) | 53.95 | 0 | 0 | |
| deBGR | 25.38 | 0 | 0 | |
Note: Topological errors are false-positive k-mers. Abundance errors are k-mers with an over count.