Table 3 Benchmarking results for simulated Oxford Nanopore reads. HC haplotype coverage, ER error rate (mismatches + indels + N’s), MC misassembled contigs proportion. NGA50 is labeled with ’-’ if the uniquely aligned blocks cover less than half of the reference length. The total sequencing coverage in this table is 20,000 ×
From: Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
| Â | #Contigs | HC (%) | N50 (bp) | NGA50 (bp) | ER (%) | MC(%) |
|---|---|---|---|---|---|---|
5-strain HIV mixture | ||||||
Strainline | 5 | 99.9 | 9702 | 9702 | 0.081 | 0.0 |
Canu | 2 | 35.8 | 18,151 | 7634 | 1.730 | 50.0 |
Wtdbg2 | 1 | 18.9 | 9046 | - | 1.327 | 0.0 |
6-strain Poliovirus mixture | ||||||
Strainline | 6 | 100.0 | 7454 | 7453 | 0.051 | 0.0 |
Canu | 1 | 16.6 | 7446 | - | 0.646 | 0.0 |
Wtdbg2 | - | - | - | - | - | - |
10-strain HCV mixture | ||||||
Strainline | 10 | 99.9 | 9294 | 9294 | 0.023 | 0.0 |
Canu | 1 | 10.0 | 9279 | - | 2.619 | 0.0 |
Wtdbg2 | 2 | 18.4 | 8567 | - | 1.336 | 0.0 |
15-strain ZIKV mixture | ||||||
Strainline | 16 | 98.3 | 10,244 | 10244 | 0.026 | 0.0 |
Canu | 1 | 6.6 | 10,251 | - | 0.459 | 0.0 |
Wtdbg2 | 3 | 17.1 | 9490 | - | 0.564 | 0.0 |
5-strain SARS-CoV-2 mixture | ||||||
Strainline | 6 | 99.9 | 29,299 | 29071 | 0.041 | 0.0 |
Canu | 10 | 66.3 | 18,003 | 9492 | 0.062 | 0.0 |
Wtdbg2 | 1 | 19.0 | 26,767 | - | 0.586 | 0.0 |