Table 3. Software tools: versions and sources.

Software tool	Version	Source
BlobToolKit	4.1.7	https://github.com/blobtoolkit/ blobtoolkit
BUSCO	5.3.2	https://gitlab.com/ezlab/busco
Hifiasm	0.16.1-r375	https://github.com/chhylp123/ hifiasm
HiGlass	1.11.6	https://github.com/higlass/higlass
Merqury	MerquryFK	https://github.com/thegenemyers/ MERQURY.FK
MitoHiFi	2	https://github.com/marcelauliano/ MitoHiFi
PretextView	0.2	https://github.com/wtsi-hpag/ PretextView
purge_dups	1.2.3	https://github.com/dfguan/purge_ dups
sanger-tol/ genomenote	v1.0	https://github.com/sanger-tol/ genomenote
sanger-tol/ readmapping	1.1.0	https://github.com/sanger-tol/ readmapping/tree/1.1.0
YaHS	1.1a.2	https://github.com/c-zhou/yahs