Table 3. Software tools used.

Software tool	Version	Source
Falcon-unzip	falcon-kit 1.2.1	( Chin et al., 2016)
SALSA2	2.1	( Ghurye et al., 2019)
scaff10x	3.0	https://github.com/wtsi-hpag/Scaff10X
arrow	GenomicConsensus 2.2.2	https://github.com/PacificBiosciences/GenomicConsensus
longranger align	2.2.2	https://support.10xgenomics.com/genome-exome/software/ pipelines/latest/advanced/other-pipelines
freebayes	1.1.0-3-g961e5f3	( Garrison & Marth, 2012)
bcftools consensus	1.9	http://samtools.github.io/bcftools/bcftools.html
Bionano Solve	3.2.2_08222018	https://bionanogenomics.com/downloads/bionano-solve/
HiGlass	1.11.6	( Kerpedjiev et al., 2018)
PretextViewer	0.0.4	https://github.com/wtsi-hpag/PretextView
gEVAL	N/A	( Chow et al., 2016)
BlobToolKit	1.2	( Challis et al., 2020)