TABLE 4.
The mean number of single nucleotide variant (SNVs), insertions and deletions detected from whole genome alignments for each LR assembly against the appropriate Unicycler reference.
| Assembly | SNVs | Insertions | Deletions | Total |
| Filtlong-Canu-Racon | 3,334 | 665 | 1,878 | 5,877 |
| Filtlong-Canu-Racon-medaka | 4,965 | 1,340 | 1,284 | 7,589 |
| Filtlong-Flye | 565 | 215 | 987 | 1,767 |
| Filtlong-Flye-medaka | 525 | 536 | 125 | 1,186 |
| Filtlong-Miniasm | 3,322 | 903 | 2,106 | 6,331 |
| Filtlong-Miniasm-medaka | 3,744 | 1,114 | 1,316 | 6,174 |
| Filtlong-Raven | 654 | 229 | 973 | 1,856 |
| Filtlong-Raven-medaka | 556 | 513 | 145 | 1,214 |
| Nanofilt-Canu-Racon | 3,805 | 815 | 2,185 | 6,805 |
| Nanofilt-Canu-Racon-medaka | 6,016 | 1,585 | 1,721 | 9,322 |
| Nanofilt-Flye | 579 | 206 | 931 | 1,716 |
| Nanofilt-Flye-medaka | 492 | 481 | 142 | 1,115 |
| Nanofilt-Miniasm | 2,627 | 647 | 1,780 | 5,054 |
| Nanofilt-Miniasm-medaka | 2,881 | 999 | 1,100 | 4,980 |
| Nanofilt-Raven | 739 | 232 | 995 | 1,966 |
| Nanofilt-Raven-medaka | 669 | 552 | 186 | 1,407 |
Data for n = 23 isolates representing isolates where Canu failed were not included in this analysis. Supplementary Table 6 summarizes individual isolate data per assembler.