Fig. 1: Construction strategy of the JG2 reference genome.

Three Japanese male volunteers (jg1a, jg1b and jg1c) provided the data for JG2. High-coverage sequencing and optical genome mapping data were generated: PacBio CLRs, Hi-C reads, Bionano optical genome maps, ONT nanopore long reads, Illumina mate-pair reads and Illumina paired-end reads. A Phased genome assemblies and scaffolding were performed for each individual using PacBio CLRs and Hi-C reads. Meta-assemblies were created within each individual. B Bionano optical genome maps were assembled, and PacBio/Hi-C-based assemblies were scaffolded with the optical genome maps in each individual. In addition, ONT long reads were assembled within each individual, then meta-assembled with the PacBio/Hi-C/Bionano-based assemblies, resulting in a draft assembly for each individual. C Draft assemblies for the three individuals were meta-assembled. White boxes indicate raw data, gray boxes indicate intermediate assemblies and rounded black boxes indicate software or operations.