The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
Open accessPublished version of a preprint
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“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]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
A global reference for human genetic variation
The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature · doi:10.1038/nature15393 · Cited by 18,247
Self-citationMinimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807
Tandem repeats finder: a program to analyze DNA sequences
Benson, G. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.2.573 · Cited by 9,374
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separationPreprint
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., & Phillippy, A. M. (2017) · Genome Research · doi:10.1101/gr.215087.116 · Cited by 7,260
Assembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2016.07.002 · Cited by 3,860
Haplotype-based variant detection from short-read sequencing
Garrison, E., & Marth, G. (2012) · arXiv · doi:10.48550/arxiv.1207.3907 · Cited by 3,700
Fast and accurate de novo genome assembly from long uncorrected readsPreprint
Vaser, R., Sović, I., Nagarajan, N., & Šikić, M. (2017) · Genome Research · doi:10.1101/gr.214270.116 · Cited by 3,059
Research works printed but not linked: 1
- Kronenberg, Z. N. et al. Extended haplotype phasing of de novo genome assemblies with FALCON-Phase. Preprint at bioRxiv https://doi.org/10.1101/327064 (2019). · DOI
Cited by
Sorted by citations
Items 201–210 of 210
Liu, Z., Xie, Z., & Li, M. (2024) · Figshare · doi:10.6084/m9.figshare.26749295
Mari, R. S., Schrinner, S., Finkers, R., Ziegler, F. M. R., Arens, P., Schmidt, M., Usadel, B., Klau, G. W., & Marschall, T. (2024) · Figshare · doi:10.6084/m9.figshare.25034391
Self-citationDeep meta-analysis of human pangenome data reveals triplication of the IGH constant gene locus
D’Addabbo, P., Cianci, R., & Frezza, D. (2026) · Discover Immunity. · doi:10.1007/s44368-026-00018-x
Manna, T., & Das, S. P. (2026) · Research Square · doi:10.21203/rs.3.rs-8814520/v1
Yue, D., Lu, Y., Chong, Y., Wu, J., Gao, Z., Ma, R., Li, K., Deng, W., & Wang, B. (2026) · Biology · doi:10.3390/biology15060465
Kidd, J. M., Souilmi, Y., Rosen, B. D., Khan, R., Weisz, D., Dudchenko, O., Aiden, E. L., Zammit, R. A., & Ballard, J. W. O. (2026) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqag035
Efficient and accurate near telomere-to-telomere haplotype reconstruction of diploid genomesPreprint
Liu, Y., Li, Y., Xu, J., 谈中正, Zhang, W., Wang, L., Xu, L., Luo, J., Zeng, X., Schönhuth, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.20.726711 · Cited by 1
Li, M., Ma, B., Shen, X., Li, C., Simakov, O., Liu, Y., & Meyer, A. (2026) · Water Biology and Security · doi:10.1016/j.watbs.2026.100681
Nanopore Ultra-Long Sequencing for FSHD: From Molecular Diagnosis to Preimplantation Genetic Testing
Li, J., Cheng, Y., Su, L., Yan, C., & Cao, Z. (2026) · Genes · doi:10.3390/genes17091104
Haplotype-resolved swine leukocyte antigen (SLA) gene typing using long-read whole genome sequencing
Boshove, A., Nunnally, A. E., Callison, S. A., Dunkelberger, J., Sevillano, C. A., Groenen, M. A. M., Jansen, C. A., & Derks, M. F. L. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1903706
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 ›
Are you an author, or do you see a problem with this page? Request a review
