Table 3. Software tools used.

Software tool	Version	Source
Falcon-unzip	falcon-kit 1.2.2	( Chin et al., 2016)
purge_dups	1.0.0	( Guan et al., 2020)
SALSA2	2.2	( Ghurye et al., 2018)
scaff10x	4.2	https://github.com/wtsi- hpag/Scaff10X
arrow	GenomicConsensus 2.3.3	https://github.com/ PacificBiosciences/ GenomicConsensus
longranger align	2.2.2	https:// support.10xgenomics. com/genome-exome/ software/pipelines/latest/ advanced/other-pipelines
freebayes	v1.1.0-3-g961e5f3	( Garrison & Marth, 2012)
bcftools consensus	1.9	http://samtools.github. io/bcftools/bcftools.html
gEVAL	2016	( Chow et al., 2016)
BlobToolKit	1	( Challis et al., 2019)
nucmer from MUMmer 3	3.0	( Kurtz et al., 2004)