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Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
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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 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.
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“These assemblies include 29 samples with long and linked read sequencing data generated entirely by the HPRC and 18 samples sequenced by other efforts16–18.”
From A draft human pangenome reference. (2023) · cites this paper as [17]
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Research works printed but not linked: 1
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Metadata
- Authors
- Human Genome Structural Variation Consortium, Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., Marijon, P., Ebler, J., Munson, K. M., Sorensen, M., Sulovari, A., Haukness, M., Ghareghani, M., Lansdorp, P. M., Paten, B., Devine, S. E., Sanders, A. D., Lee, C., Chaisson, M. J. P., Korbel, J. O., Eichler, E. E., & Marschall, T.
- Affiliations
- Heinrich Heine University Düsseldorf (DE)
- University of Washington (US)
- University of California, Santa Cruz (US)
- Max Planck Institute for Informatics (DE)
- BC Cancer Agency (CA)
- University of Maryland, Baltimore (US)
- European Molecular Biology Laboratory (DE)
- Ewha Womans University (KR)
- University of Southern California (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eichler, Evan E.
- Marschall, Tobias
- ORCID
- Porubsky, David
- Ebert, Peter
- Audano, Peter A.
- Vollger, Mitchell R.
- Harvey, William T.
- Marijon, Pierre
- Ebler, Jana
- Munson, Katherine M.
- Sorensen, Melanie
- Sulovari, Arvis
- Haukness, Marina
- Ghareghani, Maryam
- Lansdorp, Peter M.
- Paten, Benedict
- Devine, Scott E.
- Sanders, Ashley D.
- Lee, Charles
- Chaisson, Mark J. P.
- Korbel, Jan O.
- Eichler, Evan E.
- Marschall, Tobias
- Venue
- Nature Biotechnology
- Published
- 2020-12-07
- Volume
- 39
- Issue
- 3
- Pages
- 302-308
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC7954704
- OpenAlex
- W3113006061
- Cited by
- 203
- References
- 64
- Citations by year
- 2026: 12 · 2025: 24 · 2024: 34 · 2023: 44 · 2022: 39 · 2021: 36 · 2020: 13
- FWCI
- 10.87
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Biotechnology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
- The Mouseion at the JAXlibrary (Jackson Laboratory) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Howard Hughes Medical Institute
- Deutsche Forschungsgemeinschaft (391137747, 395192176, 031A533B, 031A537C, 031A534A, 031A537B, 031A535A, 031A538A, 031A532B, 031A533A)
- Bundesministerium für Bildung und Forschung (031A537C, 031A533A, 2018-2020, 031A535A, 031A538A, 031L0184, 031A534A, 031A532B, 031A533B, 031A537B)
- Ewha Womans University
- German Network for Bioinformatics Infrastructure (031A533A, 031A534A, 031A538A, 031 A535 A, 031 A537B, 031 A532B, 031 A533B, #031A537C)
- National Institutes of Health (HG007497)
- National Human Genome Research Institute (HG010169, U41HG007497, HG002385, R01HG010485, R01HG002898, U01HG010971, T32HG008345, HG002898, HG007497, U01HG010961, R01HG002385, U24HG007234, UM1HG010971, R01HG010169, T32HG000035, U24HG007497, U41HG010972, HG010971)
- National Cancer Institute (P30CA034196)
- U.S. National Library of Medicine (T32LM012419)
- H2020 European Research Council (773026)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- haplotype phasing, reference-free genome assembly, de novo genome assembly, long-read sequencing, diploid genome, structural variants, single nucleotide variants, indels
- MeSH terms
- Algorithms, Haplotypes, Humans, Parents, Puerto Rico, Genome, Human, Sequence Analysis, DNA, Single-Cell Analysis, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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