Table 3.
Prediction statistics of haplotype reconstruction methods using experimental and simulated (a) MiSeq and (b) PacBio datasets
| (a) | ||||||
|---|---|---|---|---|---|---|
| CliqueSNV | aBayesQR | PredictHaplo | ||||
| Benchmark | Precision | Recall | Precision | Recall | Precision | Recall |
| HIV9exp | 0.60 | 0.33 | 0.00 | 0.00 | 0.00 | 0.00 |
| HIV2exp | 0.66 | 1.00 | 0.11 | 0.50 | 0.50 | 0.50 |
| HIV5exp | 0.18 | 0.40 | 0.00 | 0.00 | 0.33 | 0.20 |
| HIV7sim | 1.00 | 0.71 | 1.00 | 0.42 | 0.45 | 0.71 |
| IAV10sim | 0.75 | 0.30 | 0.11 | 0.10 | 0.33 | 0.10 |
| (b) | ||||||
| CliqueSNV | 2SNV | PredictHaplo | ||||
| Benchmark | Precision | Recall | Precision | Recall | Precision | Recall |
| IAV10exp | 1.00 | 1.00 | 0.82 | 0.90 | 0.70 | 0.70 |
The precision and recall was evaluated stringently such that if a predicted haplotype has at least one mismatch to its closest answer, then that haplotype is scored as a false positive.