Table 2.
Performance on datasets with five repeat pattern sizes (1000 reads for each repeat pattern size, error rate is 15%, error distribution is 37:42:21, copy number is 10)
| Repeat pattern size | Tool | Accuracy (%) | Ave. copy number | Ave. identical base | Run time (CPU min) |
|---|---|---|---|---|---|
| TideHunter | 73.4 | 9.5 | 95.9 | 0.03 | |
| 100 bp | INC-seq | 37.7 | 2.6 | 36.5 | 12.3 |
| TRF | 70.2 | 8.4 | 67.3 | 0.2 | |
| TideHunter | 100.0 | 9.5 | 494.0 | 0.3 | |
| 500 bp | INC-seq | 87.4 | 4.2 | 453.8 | 50.8 |
| TRF | 71.9 | 7.6 | 463.0 | 1.8 | |
| TideHunter | 100.0 | 9.5 | 988.5 | 0.9 | |
| 1000 bp | INC-seq | 100.0 | 7.9 | 974.0 | 96.4 |
| TRF | 61.5 | 7.4 | 928.7 | 3.2 | |
| TideHunter | 100.0 | 9.4 | 1976.6 | 4.3 | |
| 2000 bp | INC-seq | 99.8 | 9.0 | 1955.5 | 163.4 |
| TRF | 30.0 | 5.4 | 1819.0 | 1.5 | |
| TideHunter | 100.0 | 9.4 | 2965.1 | 11.6 | |
| 3000 bp | INC-seq | 98.8 | 9.0 | 2934.2 | 300.4 |
| TRF | 0.0 | 0.0 | 0.0 | 0.8 |
Note: The best performance regarding each specific feature on each dataset.