Title

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

Document Type

Article

Publication Date

3-2021

Publication Title

Nature biotechnology

Keywords

JGM, Algorithms, Genome, Human, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Parents, Puerto Rico, Sequence Analysis, DNA, Single-Cell Analysis

JAX Source

Nat Biotechnol 2021 Mar; 39(3):302-308

Volume

39

Issue

3

First Page

302

Last Page

308

ISSN

1546-1696

PMID

33288906

DOI

https://doi.org/10.1038/s41587-020-0719-5

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.

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