Table 2. Software tools: versions and sources.

Software tool	Version	Source
Arrow	GenomicConsensus 2.3.3	https://github.com/PacificBiosciences/GenomicConsensus
bcftools consensus	1.9	http://samtools.github.io/bcftools/bcftools.html
BlobToolKit	4.0.7	https://github.com/blobtoolkit/blobtoolkit
BUSCO	5.3.2	https://gitlab.com/ezlab/busco
Dot	-	https://github.com/dnanexus/dot
falcon_unzip	falcon-kit 1.2.2	https://github.com/PacificBiosciences/FALCON_unzip
FreeBayes	v1.1.0-3-g961e5f3	https://github.com/freebayes/freebayes
gEVAL	N/A	https://geval.org.uk/
Hifiasm	0.12	https://github.com/chhylp123/hifiasm
HiGlass	1.11.6	https://github.com/higlass/higlass
Long Ranger ALIGN	2.2.2	https://support.10xgenomics.com/genome-exome/software/ pipelines/latest/advanced/other-pipelines
Merqury	MerquryFK	https://github.com/thegenemyers/MERQURY.FK
Nucmer	3.9.4alpha	http://mummer.sourceforge.net/
PBJelly		https://github.com/esrice/PBJelly
PretextView	0.2	https://github.com/wtsi-hpag/PretextView
purge_haplotigs	-	https://bitbucket.org/mroachawri/purge_haplotigs/src/master/
sanger-tol/ readmapping	1.1.0	https://github.com/sanger-tol/readmapping/tree/1.1.0
scaff10x	4.2	https://github.com/wtsi-hpag/Scaff10X
wtdbg	-	https://github.com/ruanjue/wtdbg