Table 1.

Assembly pipeline and software used.

Assembly	Software and optionsa	Version
Filtering PacBio HiFi adapters	HiFiAdapterFilt	Commit 64d1c7b
K-mer counting	Meryl (k = 21)	1
Estimation of genome size and heterozygosity	GenomeScope	2
De novo assembly (contiging)	HiFiasm (Hi-C Mode, –primary, output p_ctg.hap1, p_ctg.hap2)	0.16.1-r375
Scaffolding
Omni-C scaffolding	SALSA (-DNASE, -i 20, -p yes)	2
Gap closing	YAGCloser (-mins 2 -f 20 -mcc 2 -prt 0.25 -eft 0.2 -pld 0.2)	Commit 0e34c3b
Omni-C contact map generation
Short-read alignment	BWA-MEM (-5SP)	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	cCooler	0.8.10
Matrix balancing	hicExplorer (hicCorrectmatrix correct --filterThreshold -2 4)	3.6
Contact map visualization	HiGlass	2.1.11
	PretextMap	0.1.4
	PretextView	0.1.5
	PretextSnapshot	0.0.3
Organelle assembly
Mitogenome assembly	MitoHiFi (-r, -p 50, -o 1)	2 Commit c06ed3e
Genome quality assessment
Basic assembly metrics	QUAST (--est-ref-size)	5.0.2
Assembly completeness	BUSCO (-m geno, -l actinopterygii)	5.0.0
	Merqury	2020-01-29
Contamination screening
Local alignment tool	BLAST+	2.1
General contamination screening	BlobToolKit	2.3.3

Software citations are listed in the text.

^aOptions detailed for nondefault parameters.