De novo assembly of a haplotype-resolved human genome

The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next generation sequencing (NGS) and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15 Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and novel coding sequences and revealed their impact on genes function. This haplotype-resolved genome represents the most complete de novo genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.