Table 5. Software versions and sources.

Software	Version	Source
BEDTools	2.30.0	https://github.com/arq5x/bedtools2
BLAST	2.14.0	ftp.ncbi.nlm.nih.gov/blast/executables/blast+/
BlobToolKit	4.3.9	https://github.com/blobtoolkit/blobtoolkit
BUSCO	5.5.0	https://gitlab.com/ezlab/busco
bwa-mem2	2.2.1	https://github.com/bwa-mem2/bwa-mem2
Cooler	0.8.11	https://github.com/open2c/cooler
DIAMOND	2.1.8	https://github.com/bbuchfink/diamond
fasta_windows	0.2.4	https://github.com/tolkit/fasta_windows
FastK	1.1	https://github.com/thegenemyers/FASTK
GenomeScope2.0	2.0.1	https://github.com/tbenavi1/genomescope2.0
Gfastats	1.3.6	https://github.com/vgl-hub/gfastats
GoaT CLI	0.2.5	https://github.com/genomehubs/goat-cli
Hifiasm	0.19.8-r603	https://github.com/chhylp123/hifiasm
HiGlass	1.13.4	https://github.com/higlass/higlass
MerquryFK	1.1.2	https://github.com/thegenemyers/MERQURY.FK
Minimap2	2.24-r1122	https://github.com/lh3/minimap2
MitoHiFi	3	https://github.com/marcelauliano/MitoHiFi
MultiQC	1.14; 1.17 and 1.18	https://github.com/MultiQC/MultiQC
Nextflow	23.10.0	https://github.com/nextflow-io/nextflow
PretextSnapshot	N/A	https://github.com/sanger-tol/PretextSnapshot
PretextView	0.2.5	https://github.com/sanger-tol/PretextView
samtools	1.19.2	https://github.com/samtools/samtools
sanger-tol/ascc	0.1.0	https://github.com/sanger-tol/ascc
sanger-tol/blobtoolkit	0.6.0	https://github.com/sanger-tol/blobtoolkit
Seqtk	1.3	https://github.com/lh3/seqtk
Singularity	3.9.0	https://github.com/sylabs/singularity
TreeVal	1.2.0	https://github.com/sanger-tol/treeval
YaHS	1.2a.2	https://github.com/c-zhou/yahs