Table 3. Software tools and versions used.
| Software
tool |
Version | Source |
|---|---|---|
| Blobtoolkit | 3.3.4 | ( Challis et al., 2020) |
| freebayes | 1.3.1-17-
gaa2ace8 |
( Garrison & Marth, 2012) |
| Hifiasm | 0.15.3 | ( Cheng et al., 2021) |
| HiGlass | 1.11.6 | ( Kerpedjiev et al., 2018) |
| Long Ranger
ALIGN |
2.2.2 |
https://support.10xgenomics.com/
genome-exome/software/pipelines/ latest/advanced/other-pipelines |
| MitoHiFi | 2.0 | ( Uliano-Silva et al., 2021) |
| PretextView | 0.2 | ( Harry, 2022) |
| purge_dups | 1.2.3 | ( Guan et al., 2020) |
| YaHS | 1 | ( Zhou et al., 2022) |