Table 3. Software tools used.

Software	Version	Parameters	Source
Racon	1.4.13	Default parameters	Vaser et al., 2017
Medaka	1.2.0	Default parameters	https://github.com/nanoporetech/medaka
Pilon	1.23	Default parameters	Walker et al., 2014
Salsa	2.3	-m CLEAN -e GATC,GANTC,CTNAG,TTAA	Ghurye et al., 2019
BlobToolKit	2.6.4 (BTK pipeline) 3.1.0 (Blobtoolkit)	Default parameters	Challis et al., 2020
nf-core/hic	1.1.0	--restriction_site ‘^GATC,G^ANTC,C^TNAG,T^TAA’ --ligation_site ‘GATCGATC,GANTGATC,GANTANTC,GATCANTC’ --skip_tads	Servant and Peltzer, 2019
Juicer Tools	2.13.06	Default parameters	Durand et al., 2016b
Juice Box	2.13.06	Default parameters	Durand et al., 2016a
Redbean	2.5	Default parameters	Ruan and Li, 2019
LongStitch	1.0.1	tigmint-ntLink-arks G=2e9 z=100	Coombe et al., 2021
Jupiter Plot	1.0	ng=98	Chu, 2018
Busco	5.2.2	-l sauropsida_odb10	Manni et al., 2021
Quast	5.0.2	Default parameters	Gurevich et al., 2013
RepeatMasker	4.1.5	-species “Caretta caretta”	Tarailo‐Graovac & Chen, 2009