Table 4. Software tools: versions and sources.

Software tool	Version	Source
BLAST	2.14.0	ftp://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
DIAMOND	2.1.8	https://github.com/bbuchfink/diamond
fasta_windows	0.2.4	https://github.com/tolkit/fasta_windows
FastK	666652151335353eef2fcd58880bcef5bc2928e1	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	0.16.1-r375	https://github.com/chhylp123/hifiasm
HiGlass	44086069ee7d4d3f6f3f0012569789ec138f42b8 4aa44357826c0b6753eb28de	https://github.com/higlass/higlass
MerquryFK	d00d98157618f4e8d1a9190026b19b471055b 22e	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
PretextView	0.2.5	https://github.com/sanger-tol/PretextView
PretextSnapshot	-	https://github.com/sanger-tol/PretextSnapshot
purge_dups	1.2.5	https://github.com/dfguan/purge_dups
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