Supplemental Materials for Schall et al., 2023

Basecalling of JARDRD000000000, JARDRE000000000, and JARDRF000000000 were conducted using Guppy v5.0.11 with  configuration file dna_r9.4.1_450bps_hac_prom.cfg. Publically available fastq files were utilized for DAOUOP000000000. Initial assembly of reads were generated using Flye v2.9, with standard settings. This was followed by three rounds of assembly polishing with standard settings with Racon v1.5.0,  

(Vaser et al. 2017). Sequence correction was applied with Medaka v1.6.1, followed by assembly correction with RagTag v2.1.0. Scaffolding of the assembly to the CanFam4 German Shepherd genome (UU_Cfam_GSD_1.0, GCF_011100685.1), supplemented with three Y chromosome sequences from a Labrador Retriever (ROS_Cfam_1.0, GCF_014441545.1), was conducted using RagTag. Closure of assembly gaps was completed using TGS-GapCloser v1.0.1 (RRID:SCR_017633), with standard settings. Final polishing of the assembly with short-read Illumina data was conducted using NextPolish v1.4.1 using standard settings. Removal of contigs with unusual sequence coverage using the package Purge_Haplotigs v1.1.2.  Gene annotations in GTF format were converted from UU_Cfam_GSD_1.0 coordinates to each assembly using Liftoff v1.6.3.