Table 3. Software tools used.

Software tool	Version	Source
Hifiasm	0.15.3-r339	Cheng et al., 2021
purge_dups	1.2.3	Guan et al., 2020
SALSA	3.0	Ghurye et al., 2019
longranger align	2.2.2	https://support.10xgenomics.com/genome- exome/software/pipelines/latest/advanced/ other-pipelines
freebayes	1.3.1-17- gaa2ace8	Garrison & Marth, 2012
MitoHiFi	2.0	Uliano-Silva et al., 2021
HiGlass	1.11.6	Kerpedjiev et al., 2018
PretextView	0.2.x	https://github.com/wtsi-hpag/PretextView
BlobToolKit	3.0.5	Challis et al., 2020