Table 3. Software tools and versions used.

Software tool	Version	Source
BlobToolKit	3.4.0	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
SALSA	2.2	Ghurye et al., 2019