Table 1.

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

Assembly	Software and any non-default options	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 (HiC Mode, –primary, output p_ctg.hap1, p_ctg.hap2)	0.16.1-r375
Scaffolding
Omni-C data alignment	Arima Genomics Mapping Pipeline	Commit 2e74ea4
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	cooler	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
Manual curation tools	Rapid curation pipeline (Wellcome Trust Sanger Institute, Genome Reference Informatics Team)	Commit 4ddca450
Genome quality assessment
Basic assembly metrics	QUAST (--est-ref-size)	5.0.2
Assembly completeness	BUSCO (-m geno, -l metazoa)	5.0.0
	Merqury	2020-01-29
Contamination screening
Local alignment tool	BLAST+ (-db nt, -outfmt “6 qseqid staxids bitscore std,” -max_target_seqs 1, -max_hsps 1, -evalue 1e-25)	2.15
General contamination screening	BlobToolKit (HiFi coverage, BUSCO=metazoa, NCBI Taxa ID=2067768)	2.3.3
Mitochondrial assembly
Mitochondrial genome assembly	MitoHiFi (-r, -p 90, -o 1, -a animal) Reference: Arion flagellus (NCBI:NC_073101.1)	2.2
Repeat analysis
Identification of repeat elements	RepeatModeler (Dfam database (version 3.8))	2.0.6
Annotation of repeat elements	RepeatMasker	4.1.7-p1
Annotation of tandem repeats	TRF	4.09.1