Protocol for haplotype-resolved genome comparison and individual-specific allele expression quantification

The comparison of haplotype-resolved genomes and the analysis of allele-specific expression (ASE) are crucial for a deeper understanding of phenotypic variation. Here, we present a protocol for both haplotype-resolved genome comparison and ASE analysis. We've also expanded this protocol to allow for accurate ASE analysis across multiple tissues and individuals. This protocol offers potential for investigating the relationship between gene expression and genome diversity, as well as for applications in allele-specific quantitative trait locus studies.