Table 1.
Comparison of ab initio repeat finders
| Tool | Run time (mins) | Sensitivity (% bp) | Portion (% bp) of dataset classified as repetitive | Potential novel repeats (% bp) | Number of families | Average length of family consensus sequence | Total bases in consensus sequence library |
|---|---|---|---|---|---|---|---|
| Simulated reads (650 bp each; Dataset: 3000 Kbp × 6 = 18 000 Kbp) | |||||||
| Recon | 3866.17 | 38.1 | 25.8 | 15.7 | 1291 | 485 | 626 157 |
| ReAS | 7.14 | 50.1 | 15.3 | 2.1 | 181 | 443 | 80 235 |
| Chromosome segment (Dataset: 3000 Kbp) | |||||||
| RepeatGluer | 4.55 | 99.9 | 99.3 | 72.2 | 38 | 157 451 | 5 983 148 |
| RepeatScout | 4.76 | 26.2 | 7.3 | 0.3 | 45 | 302 | 13 614 |
| RepeatFinder | 0.38 | 32.7 | 10.3 | 1.4 | 1000 | 153 | 153 531 |
| PILER | 0.11 | 0.04 | >0.1 | 0.0 | 1 | 420 | 420 |
| Chromosome (Dataset: 27 757 Kbp) | |||||||
| RepeatScout | 112.11 | 84.3 | 39.7 | 4.4 | 657 | 860 | 565 020 |
| RepeatFinder | 59.48 | 85.3 | 44.6 | 8.9 | 25 113 | 252 | 6 347 059 |
| PILER | 3.45 | 38.3 | 17.5 | 1.4 | 41 | 2767 | 113 473 |