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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
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Journal Article
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
2021
Overview
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-fidelity
3
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.
Assembly of haplotype-resolved human genomes is achieved by combining short and long reads.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ Analysis
/ Assembly
/ Biomedical and Life Sciences
/ Biomedical Engineering/Biotechnology
/ Diploids
/ Genomes
/ Genomics
/ High-Throughput Nucleotide Sequencing - methods
/ Humans
/ Letter
/ Methods
/ Parents
/ Porosity
/ Sequence Analysis, DNA - methods
/ Single-Cell Analysis - methods
/ Workflow
