The reference genome of the human diploid cell line RPE-1 We have sequenced the diploid genome of the human diploid laboratory cell line RPE-1. This near complete, fully phased can be used as matched reference genomes to analyze sequencing data generated from the same cell line, an approach we refer to as isogenomic reference genome. The improvement in alignment quality using matched reads-reference enables high-precision mapping for profiling phased epigenome and methylome. This proof-of-concept calls for a comprehensive catalog of complete assemblies for commonly used cells for a widespread application of isogenomic reference genomes to enable high-precision multi-omics analyses. The Zenodo repository contains supplemental information not available in the GitHub repository.