Table 4. Software tools: versions and sources.

Software tool	Version	Source
BEDTools	2.30.0	https://github.com/arq5x/bedtools2
BLAST	2.14.0	ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/
BlobToolKit	4.3.7	https://github.com/blobtoolkit/blobtoolkit
BUSCO	5.4.3 and 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	427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c	https://github.com/thegenemyers/FASTK
Gfastats	1.3.6	https://github.com/vgl-hub/gfastats
GoaT CLI	0.2.5	https://github.com/genomehubs/goat-cli
Hifiasm	0.19.5-r587	https://github.com/chhylp123/hifiasm
HiGlass	44086069ee7d4d3f6f3f0012569789ec138f42b84 aa44357826c0b6753eb28de	https://github.com/higlass/higlass
Merqury.FK	d00d98157618f4e8d1a9190026b19b471055b22e	https://github.com/thegenemyers/MERQURY.FK
MitoHiFi	3	https://github.com/marcelauliano/MitoHiFi
MultiQC	1.14, 1.17, and 1.18	https://github.com/MultiQC/MultiQC
NCBI Datasets	15.12.0	https://github.com/ncbi/datasets
Nextflow	23.04.0-5857	https://github.com/nextflow-io/nextflow
PretextView	0.2	https://github.com/sanger-tol/PretextView
purge_dups	1.2.5	https://github.com/dfguan/purge_dups
samtools	1.16.1, 1.17, and 1.18	https://github.com/samtools/samtools
sanger-tol/ascc	-	https://github.com/sanger-tol/ascc
sanger-tol/ genomenote	1.1.1	https://github.com/sanger-tol/genomenote
sanger-tol/ readmapping	1.2.1	https://github.com/sanger-tol/readmapping
Seqtk	1.3	https://github.com/lh3/seqtk
Singularity	3.9.0	https://github.com/sylabs/singularity
TreeVal	1.0.0	https://github.com/sanger-tol/treeval
YaHS	1.2a.2	https://github.com/c-zhou/yahs