From: LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo
Tool | Total | TP | GT | FP | Sensitivity | Precision | F1 | Time (hr:min:sec) | Memory (GB) |
---|---|---|---|---|---|---|---|---|---|
A. thaliana | |||||||||
LTR_Finder | 399 | 106 | 248 | 0 | 0.427 | 1.000 | 0.599 | 0:30:46 | 0.86 |
LTRharvest | 2301 | 180 | 248 | 6 | 0.726 | 0.968 | 0.829 | 0:01:08 | 0.24 |
LtrDetector | 1714 | 187 | 248 | 9 | 0.754 | 0.954 | 0.842 | 0:04:02 | 4.45 |
O. sativa | |||||||||
LTR_Finder | 5324 | 1163 | 1760 | 14 | 0.661 | 0.988 | 0.792 | 5:19:03 | 0.95 |
LTRharvest | 9761 | 1392 | 1760 | 182 | 0.791 | 0.884 | 0.835 | 0:03:09 | 0.34 |
LtrDetector | 7343 | 1442 | 1760 | 119 | 0.819 | 0.924 | 0.868 | 0:15:30 | 5.31 |
S. bicolor | |||||||||
LTR_Finder | 11734 | 4219 | 6565 | 67 | 0.643 | 0.984 | 0.778 | 10:43:26 | 1.62 |
LTRharvest | 22700 | 4476 | 6565 | 502 | 0.682 | 0.899 | 0.776 | 0:04:23 | 0.60 |
LtrDetector | 24682 | 5285 | 6565 | 214 | 0.805 | 0.961 | 0.876 | 1:10:47 | 6.1 |
G. max | |||||||||
LTR_Finder | 12141 | 1748 | 3130 | 7 | 0.558 | 0.996 | 0.716 | 25:18:21 | 1.88 |
LTRharvest | 29016 | 2171 | 3130 | 20 | 0.694 | 0.991 | 0.816 | 0:09:35 | 0.48 |
LtrDetector | 25537 | 2542 | 3130 | 12 | 0.812 | 0.995 | 0.894 | 0:43:06 | 6.11 |
Z. mays | |||||||||
LTR_Finder | 60860 | 11411 | 16839 | 13 | 0.678 | 0.999 | 0.807 | 111:21:37 | 12.36 |
LTRharvest | 101943 | 11244 | 16839 | 102 | 0.668 | 0.991 | 0.798 | 0:15:00 | 2.36 |
LtrDetector | 116923 | 13122 | 16839 | 71 | 0.779 | 0.995 | 0.874 | 5:53:08 | 9.62 |
H. vulgare | |||||||||
LTR_Finder | – | – | – | – | – | – | – | – | – |
LTRharvest | 207016 | 4378 | 9164 | 492 | 0.478 | 0.899 | 0.624 | 1:33:29 * | 5.12 |
LtrDetector | 213367 | 6824 | 9164 | 199 | 0.745 | 0.972 | 0.843 | 17:24:04** | 14.15 |
Total (Excluding H. vulgare) | |||||||||
LTR_Finder | 90458 | 18647 | 28542 | 101 | 0.653 | 0.995 | 0.789 | 153:13:13 | – |
LTRharvest | 165721 | 19463 | 28542 | 812 | 0.682 | 0.960 | 0.797 | 0:33:15 | – |
LtrDetector | 176197 | 22578 | 28542 | 425 | 0.791 | 0.982 | 0.876 | 8:06:33 | – |
Total (Including H. vulgare) | |||||||||
LTRharvest | 372737 | 23841 | 37706 | 1304 | 0.632 | 0.948 | 0.759 | 02:06:44 | – |
LtrDetector | 389564 | 29402 | 37706 | 624 | 0.780 | 0.979 | 0.868 | 25:30:37 | – |