Table 1.

Assembly pipeline and software usage. Software citations are listed in the text

Assembly	Software	Version
Filtering PacBio HiFi adapters	HiFiAdapterFilt https://github.com/sheinasim/HiFiAdapterFilt	Commit 64d1c7b
K-mer counting	Meryl	1
Estimation of genome size and heterozygosity	GenomeScope	2
De novo assembly (contiging)	HiFiasm	0.13-r308
Long read, genome-genome alignment	minimap2	2.16
Remove low-coverage, duplicated contigs	purge_dups	1.0.1
Scaffolding
Hi-C mapping for SALSA	Arima Genomics mapping pipeline https://github.com/ArimaGenomics/mapping_pipeline	Commit 2e74ea4
Hi-C Scaffolding	SALSA	2
Gap closing	YAGCloser https://github.com/merlyescalona/yagcloser	Commit 20e2769
Hi-C contact map generation
Short-read alignment	bwa	0.7.17-r1188
SAM/BAM processing	samtools	1.11
SAM/BAM filtering	pairtools	0.3.0
Pairs indexing	pairix	0.3.7
Matrix generation	Cooler	0.8.10
Matrix balancing	hicExplorer	3.6
Contact map visualization	HiGlass	2.1.11
	PretextMap	0.1.4
	PretextView	0.1.5
	PretextSnapshot	0.0.3
Organelle assembly
Sequence similarity search	BLAST+	2.10
Long read alignment	Pbmm2 (https://github.com/PacificBiosciences/pbmm2)	1.4.0
Variant calling and consensus	bcftools	1.11-5-g9c15769
Extraction of sequences	seqtk	1.3-r115-dirty
Circular-aware long-read alignment	racon	1.4.19
Sequence polishing	raptor	0.20.3-171e0f1
Sequence alignment	lastz	1.04.08
Gene annotation	MitoFinder	1.4
Genome quality assessment
Basic assembly metrics	QUAST	5.0.2
Assembly completeness	BUSCO	5.0.0
	Merqury	1
Contamination screening
General contamination screening	BlobToolKit	2.3.3