Table 6 Benchmarking results for 5-strain HIV mixture (PacBio CLR reads) with varying sequencing coverage. HC haplotype coverage, ER error rate (mismatches + indels + N’s), MC misassembled contigs proportion
From: Strainline: full-length de novo viral haplotype reconstruction from noisy long reads
| Â | #Contigs | HC (%) | N50 (bp) | NGA50 (bp) | ER (%) | MC(%) |
|---|---|---|---|---|---|---|
500 × | ||||||
Strainline | 7 | 78.4 | 9517 | 9545 | 1.603 | 0.0 |
Canu | 4 | 32.9 | 6766 | 5281 | 1.447 | 0.0 |
Wtdbg2 | 1 | 18.0 | 8687 | - | 2.295 | 0.0 |
1000 × | ||||||
Strainline | 5 | 79.2 | 9557 | 9554 | 1.069 | 0.0 |
Canu | 5 | 63.6 | 7207 | 7139 | 1.087 | 0.0 |
Wtdbg2 | 1 | 13.5 | 6516 | - | 1.520 | 0.0 |
2000 × | ||||||
Strainline | 6 | 99.3 | 9644 | 9614 | 0.675 | 0.0 |
Canu | 5 | 67.4 | 8193 | 7544 | 0.416 | 20.0 |
Wtdbg2 | 1 | 16.0 | 7741 | - | 1.103 | 0.0 |
5000 × | ||||||
Strainline | 5 | 99.7 | 9690 | 9686 | 0.311 | 0.0 |
Canu | 4 | 69.3 | 8264 | 8001 | 0.537 | 25.0 |
Wtdbg2 | 1 | 16.5 | 7950 | - | 2.115 | 0.0 |
10000 × | ||||||
Strainline | 5 | 99.8 | 9696 | 9691 | 0.184 | 0.0 |
Canu | 4 | 71.7 | 8844 | 8524 | 0.446 | 25.0 |
Wtdbg2 | 1 | 15.6 | 7528 | - | 2.777 | 0.0 |
20000 × | ||||||
Strainline | 5 | 99.9 | 9697 | 9697 | 0.002 | 0.0 |
Canu | 5 | 84.5 | 8227 | 8170 | 0.409 | 20.0 |
Wtdbg2 | 1 | 15.5 | 7419 | - | 1.820 | 0.0 |