While next-generation sequencing (NGS) has dramatically increased the availability of genomic data, phased genome assembly and structural variant (SV) analyses are limited by NGS read lengths. Long-read sequencing from Pacific Biosciences (PacBio) and NGS barcoding from 10X Genomics (10X) hold the potential for far more comprehensive views of individual genomes. Here we present MsPAC, a tool that combines both technologies to partition reads, assemble haplotypes (via existing software), and convert assemblies into high-quality, phased SV predictions. MsPAC represents a framework for haplotype-resolved SV calls that moves one step closer to fully resolved, diploid genomes.