Using what later become known as the GenomeFocus workflow, assembly of the contigs was done using smartdenovo with an estimated 52x coverage of Oxford Nanopore reads. Contigs were polished with racon, using two rounds of long-read data and one round of Illumina short read data (10x coverage). The GBS-based genetic map for the LR-66 RIL population was used to assign contigs to chromosome bins. Two lanes of HiC data were generated, and used to order and orient contigs within each bin using ALLHiC, as well as using the software's rescue mode to assign contigs that contained no markers in the genetic map to bins. The HiC data was also passed through SALSA and used to break several chimeric contigs. Pseudomolecule assemblies were individually visualized and manual corrections to fix telomere tethering issues made using Juicebox.