Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Human Genome Structural Variation Consortium, David Porubsky, Peter Ebert, Peter A Audano, Mitchell R Vollger, William T Harvey, Pierre Marijon, Jana Ebler, Katherine M Munson, Melanie Sorensen, Arvis Sulovari, Marina Haukness, Maryam Ghareghani, Peter M Lansdorp, Benedict Paten, Scott E Devine, Ashley D Sanders, Charles Lee, Mark J P Chaisson, Jan O KorbelEvan E Eichler, Tobias Marschall

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Abstract

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 sequencing1,2 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.

Original languageEnglish
Pages (from-to)302-308
Number of pages13
JournalNature Biotechnology
Volume39
Early online date7-Dec-2020
DOIs
Publication statusPublished - Mar-2021
Externally publishedYes

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