Table 5 Absolute and relative errors of estimated haplotype abundances by Strainline on different virus mixtures. For each dataset, we present the average error over all assembled strains. Note that for the SARS-CoV-2 (SRP250446) real sample, the abundance estimation error is not shown because the ground truth is unknown. AFE absolute frequency error, RFE relative frequency error
From: Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
Datasets | AFE (%) | RFE (%) |
|---|---|---|
Simulated PacBio CLR | ||
5-strain HIV | 0.04 | 0.18 |
6-strain Poliovirus | 2.17 | 48.35 |
10-strain HCV | 0.06 | 0.80 |
15-strain ZIKV | 0.18 | 4.93 |
5-strain SARS-CoV-2 | 3.40 | 17.49 |
Simulated ONT | ||
5-strain HIV | 0.27 | 1.48 |
6-strain Poliovirus | 2.30 | 51.18 |
10-strain HCV | 0.28 | 3.05 |
15-strain ZIKV | 0.28 | 6.10 |
5-strain SARS-CoV-2 | 4.14 | 20.60 |
Experimental ONT | ||
5-strain PVY | 4.48 | 23.07 |