Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing^1,2 with continuous long-read or high-fidelity³ sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.

人类基因组通常被组装为缺乏亲本单倍型信息的共有序列。在这里，我们描述了二倍体从头基因组组装的无参考工作流程，该工作流程将单细胞链测序^1,2的染色体范围定相和支架功能与连续长读长或高保真³测序数据相结合。采用这种策略，我们在缺乏亲代数据的情况下，为波多黎各血统个体（HG00733）的每个单倍型产生了完全定相的从头基因组组装。组装准确（质量值 > 40）、高度连续（重叠群 N50 > 23 Mbp），转换错误率低 (0.17%)，提供完全定相的单核苷酸变体、插入缺失和结构变体。 Oxford Nanopore Technologies 和 Pacific Biosciences 定相组装的比较确定了 154 个区域，这些区域是重叠群断裂的优先位点，无论测序技术或定相算法如何。