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

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Item Type:Article
Title:Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
Creators Name:Porubsky, D. and Ebert, P. and Audano, P.A. and Vollger, M.R. and Harvey, W.T. and Marijon, P. and Ebler, J. and Munson, K.M. and Sorensen, M. and Sulovari, A. and Haukness, M. and Ghareghani, M. and Lansdorp, P.M. and Paten, B. and Devine, S.E. and Sanders, A.D. and Lee, C. and Chaisson, M.J.P. and Korbel, J.O. and Eichler, E.E. and Marschall, T.
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 sequencing with continuous long-read or high-fidelity 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.
Keywords:Algorithms, DNA Sequence Analysis, Haplotypes, High-Throughput Nucleotide Sequencing, Human Genome, Parents, Puerto Rico, Single-Cell Analysis
Source:Nature Biotechnology
Publisher:Nature Publishing Group
Page Range:302-308
Date:March 2021
Official Publication:https://doi.org/10.1038/s41587-020-0719-5
PubMed:View item in PubMed

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