Cited by 210Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalitiesSingle-cell and spatial transcriptomics

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 access

Human Genome Structural Variation Consortium, 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·2021·Nature Biotechnology

DOI 10.1038/s41587-020-0719-5PMC PMC7954704

Published version of a preprint

Open this paper in CoChat — free account Open PDF

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.

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

Crossref · 10.1038/s41587-020-0719-5

Cites

66 of 66 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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-citation
Minimap2: 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

Show all 64 references

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

Sorted by citations

Items 101–200 of 210

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome BrowserPreprint
Zhuo, X., Hsu, S., Purushotham, D., Kuntala, P. K., Harrison, J. K., Du, A. Y., Chen, S., Li, D., & Wang, T. (2023) · Genome Research · doi:10.1101/gr.277550.122 · Cited by 12
Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing
Henglin, M., Ghareghani, M., Harvey, W. T., Porubskỳ, D., Koren, S., Eichler, E. E., Ebert, P., & Marschall, T. (2024) · Genome biology · doi:10.1186/s13059-024-03409-1 · Cited by 11
Self-citation
Near-complete Middle Eastern genomes refine autozygosity and enhance disease-causing and population-specific variant discovery
Ghorbani, M., Moosa, S., Siddig, Z., Farhad, R., Naeem, H., Harvey, W. T., Mastrorosa, F. K., Munson, K. M., Razali, R., ALIYEV, E. E., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02173-7 · Cited by 13
Self-citation
Applications of advanced technologies for detecting genomic structural variation
Laufer, V. A., Glover, T. W., & Wilson, T. E. (2023) · Mutation Research/Reviews in Mutation Research · doi:10.1016/j.mrrev.2023.108475 · Cited by 10
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data
Tian, H., Hu, Q., Lu, H.-Y., & Li, Z. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.903185 · Cited by 10
Chromosome‐level haplotype‐resolved genome assembly provides insights into the highly heterozygous genome of Italian ryegrass ( Lolium multiflorum Lam.)
Chen, Y., Kiesbauer, J., Copetti, D., Frei, D., Frey, J. E., Grieder, C., Kölliker, R., & Studer, B. (2025) · The Plant Genome · doi:10.1002/tpg2.70079 · Cited by 12
Personalized genome structure via single gamete sequencing
Lyu, R., Tsui, V., McCarthy, D. J., & Crismani, W. (2021) · Genome biology · doi:10.1186/s13059-021-02327-w · Cited by 12
A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxiaPreprint
Rafehi, H., Fearnley, L. G., Read, J. L., Snell, P., Davies, K. C., Scott, L. W., Gillies, G., Thompson, G. C., Field, T. A., Eldo, A., et al. (2025) · Genome Research · doi:10.1101/gr.279634.124 · Cited by 13
Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly
Darian, J. C., Kundu, R., Rajaby, R., & Sung, W.-K. K. (2024) · Nature Methods · doi:10.1038/s41592-023-02141-1 · Cited by 9
Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing
Deynze, K. V., Mumm, C., Maltby, C. J., Switzenberg, J. A., Todd, P. K., & Boyle, A. P. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1202 · Cited by 9
Benchmarking multi-platform sequencing technologies for human genome assembly
Wang, J., Veldsman, W. P., Fang, X., Huang, Y., Xie, X., Lü, A., & Zhang, L. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad300 · Cited by 7
Limitations of current high-throughput sequencing technologies lead to biased expression estimates of endogenous retroviral elements
Kitsou, K., Katzourakis, A., & Magiorkinis, G. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae081 · Cited by 8
Critical length in long-read resequencing
Coster, W. D., Stražišar, M., & Rijk, P. D. (2020) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqz027 · Cited by 8
Genome assembly in the telomere-to-telomere eraPreprint
Li, H., & Durbin, R. M. (2023) · PubMed · doi:10.48550/arxiv.2308.07877 · Cited by 9
Locityper: targeted genotyping of complex polymorphic genesPreprint
Prodanov, T., Plender, E. G., Seebohm, G., Meuth, S. G., Eichler, E. E., & Marschall, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.05.03.592358 · Cited by 8
Self-citation
High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq
Chovanec, P., Ridgley, T., & Yin, Y. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag119 · Cited by 10
Comparative genome analysis using sample-specific string detection in accurate long reads
Khorsand, P., Denti, L., Bonizzoni, P., Chikhi, R., & Hormozdiari, F. (2021) · Bioinformatics Advances · doi:10.1093/bioadv/vbab005 · Cited by 9
The telomere-to-telomere, gapless, phased diploid genome and methylome of the green alga Scenedesmus obliquus UTEX 3031 reveals significant heterozygosity and functional separation of the haplotypes
Biondi, T. C., Kruse, C. P. S., Koehler, S. I., Kwon, T., Davis, A. K., Eng, W., Kunde, Y. A., Gleasner, C. D., Mak, K. Y., Polle, J. E. W., et al. (2022) · Algal Research · doi:10.1016/j.algal.2024.103431 · Cited by 9
Missing heritability of Wilson disease: a search for the uncharacterized mutations
Roy, S., Ghosh, S., Ray, J., Ray, K., & Sengupta, M. (2022) · Mammalian Genome · doi:10.1007/s00335-022-09971-y · Cited by 7
The phased chromosome-scale genome of yellowhorn sheds light on the mechanism of petal color change
Bi, Q., Wang, M., Li, J., Lian, J., Niu, Y., Cui, Y., Liu, X., Yu, H., & Wang, L. (2023) · Horticultural Plant Journal · doi:10.1016/j.hpj.2023.05.010 · Cited by 7
Hybrid-hybrid correction of errors in long reads with HERO
Kang, X., Xu, J., Luo, X. L., & Schönhuth, A. (2023) · Genome biology · doi:10.1186/s13059-023-03112-7 · Cited by 8
Thousands of human mutation clusters are explained by short-range template switchingPreprint
Löytynoja, A. (2022) · Genome Research · doi:10.1101/gr.276478.121 · Cited by 6
Chromosome-level haplotype-resolved assembly of highly heterozygous grass genomes with PhaseGrass
Chen, Y., Copetti, D., Kölliker, R., Mascher, M., Himmelbach, A., Stein, N., & Studer, B. (2025) · Nature Communications · doi:10.1038/s41467-025-66377-5 · Cited by 6
Processes shaping cancer genomes – From mitotic defects to chromosomal rearrangements
Keuper, K., Wieland, A., Räschle, M., & Štorchová, Z. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103207 · Cited by 6
Improving long-read consensus sequencing accuracy with deep learningPreprint
Lal, A., Brown, M., Mohan, R. R., Daw, J., Drake, J. P., & Israeli, J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.28.450238 · Cited by 6
A T2T-CHM13 recombination map and globally diverse haplotype reference panel improves phasing and imputationPreprint
Lalli, J. L., Bortvin, A. N., McCoy, R. C., & Werling, D. M. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.24.639687 · Cited by 9
Haplotype-resolved assembly of a pig genome using single-sperm sequencing
Niu, Y., Fan, X., Yang, Y., Li, J., Lian, J., Wang, L., Zhang, Y., Tang, Y., & Tang, Z. (2024) · Communications Biology · doi:10.1038/s42003-024-06397-x · Cited by 5
Exploring intra‐ and intergenomic variation in haplotype‐resolved pangenomes
Jonkheer, E. M., de Ridder, D., van der Lee, T., de Haan, J. R., Berke, L., & Smit, S. (2025) · Plant Biotechnology Journal · doi:10.1111/pbi.14545 · Cited by 5
Identification and correction of phase switches with Hi-C data in the Nanopore and HiFi chromosome-scale assemblies of the dikaryotic leaf rust fungus Puccinia triticinaPreprint
Duan, H., Jones, A., Hewitt, T., Mackenzie, A., Hu, Y., Sharp, A., Lewis, D., Mago, R., Upadhyaya, N. M., Rathjen, J. P., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.28.441890 · Cited by 5
Inversion polymorphism in a complete human genome assemblyPreprint
Porubskỳ, D., Harvey, W. T., Rozanski, A. N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A. D., Marschall, T., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.06.511148 · Cited by 5
Self-citation
Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research
Olbrich, M. R., Bartels, L., & Wohlers, I. (2024) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2024.1384497 · Cited by 4
Simultaneous de novo calling and phasing of genetic variants at chromosome-scale using NanoStrand-seq
Bai, X., Chen, Z., Chen, K., Wu, Z., Wang, R., Liu, J., Chang, L., Wen, L., & Tang, F. (2024) · Cell Discovery · doi:10.1038/s41421-024-00694-9 · Cited by 4
Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping
Gan, P. H. P., Yeo, H. L., Hajis, M. I. B., Maulana, Y., Ng, A. Q. H., Ramanto, K. N., Dewanggana, M. N., Irwanto, A. K., Sani, L. L., Goh, L. L., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-22941-z · Cited by 4
Comparisons of performances of structural variants detection algorithms in solitary or combination strategy
Duan, D., Cheng, C.-Y., Huang, Y.-S., Chung, A., Chen, P.-X., Chen, Y.-A., Hsu, J. S., & Chen, P. (2025) · PLoS ONE · doi:10.1371/journal.pone.0314982 · Cited by 4
A Method for Localizing Non-Reference Sequences to the Human Genome.
Chrisman, B., Paskov, K. M., He, C., Jung, J.-Y., Stockham, N., Washington, P. Y., & Wall, D. P. (2022) · PubMed · Cited by 4
SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs
Tolstoganov, I., Chen, Z., Pevzner, P. A., & Korobeynikov, A. (2024) · PeerJ · doi:10.7717/peerj.18050 · Cited by 3
Chromosome-Scale Genome Assembly of the African Giant Pouched Rat (Cricetomys Ansorgei) and Evolutionary Analysis Reveals Evidence of Olfactory Specialization
Bentz, E. J., & Ophir, A. G. (2022) · Genomics · doi:10.1016/j.ygeno.2022.110521 · Cited by 4
Haplotype-aware single-cell multiomics uncovers functional effects of somatic structural variationPreprint
Jeong, H., Grimes, K., Bruch, P., Rausch, T., Hasenfeld, P., Sabarinathan, R., Porubskỳ, D., Herbst, S. A., Erarslan-Uysal, B., Jann, J.-C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.11.468039 · Cited by 4
Self-citation
Generating multiple alignments on a pangenomic scale
Olbrich, J., Büchler, T., & Ohlebusch, E. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf104 · Cited by 4
A mapping platform for mitotic crossover by single-cell multi-omics
Chovanec, P., & Yin, Y. A. (2021) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2021.08.017 · Cited by 3
Constructing founder sets under allelic and non-allelic homologous recombination
Bonnet, K., Marschall, T., & Doerr, D. (2023) · Algorithms for Molecular Biology · doi:10.1186/s13015-023-00241-3 · Cited by 3
Self-citation
gcaPDA: a haplotype-resolved diploid assembler
Xie, M., Yang, L., Jiang, C., Wu, S., Luo, C., Yang, X., He, L., Chen, S., Deng, T., Ye, M., et al. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04591-4 · Cited by 3
Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR SuitePreprint
Lin, M.-J., Lin, Y.-C., Chen, N.-C., Luo, A. C., Lai, S.-K., Hsu, C., Hsu, J. S., Chen, C., Yang, W., & Chen, P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.27.399857 · Cited by 3
Computational Methods for Chromosome-Scale Haplotype ReconstructionPreprint
Garg, S. (2021) · Preprints.org · doi:10.20944/preprints202101.0116.v1 · Cited by 3
RAmbler resolves complex repeats in human Chromosomes 8, 19, and XPreprint
Chakravarty, S., Logsdon, G. A., & Lonardi, S. (2025) · Genome Research · doi:10.1101/gr.279308.124 · Cited by 3
Strand-seq and the future of personalized genomics
Hanlon, V. C. T., & Lansdorp, P. (2026) · Nature Genetics · doi:10.1038/s41588-026-02548-4 · Cited by 1
Self-citation
The X Chromosome from Telomere to Telomere: Key Achievements and Future Opportunities
Heard, É., Johnson, A. D., Korbel, J. O., Lee, C., Snyder, M. P., & Sturgill, D. M. (2021) · Faculty Reviews · doi:10.12703/r-01-000001 · Cited by 2
Self-citation
Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data
Zhang, J., Nie, F., Luo, F., & Wang, J. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae712 · Cited by 2
An integrated personal and population-based Egyptian genome referencePreprint
Wohlers, I., Künstner, A., Munz, M., Olbrich, M. R., Fähnrich, A., Calonga-Solís, V., Ma, C., Hirose, M., El-Mosallamy, S., Salama, M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/681254 · Cited by 2
Improving variant calling using population data and deep learningPreprint
Chen, N.-C., Kolesnikov, A., Goel, S., Yun, T., Chang, P.-C., & Carroll, A. W. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.06.425550 · Cited by 2
The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivarPreprint
Qi, W., Lim, Y., Patrignani, A., Schläpfer, P., Bratus-Neuenschwander, A., Grüter, S., Chanez, C., Rodde, N., Prat, E., Vautrin, S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.16.468774 · Cited by 2
Fixing reference errors efficiently improves sequencing resultsPreprint
Behera, S., LeFaive, J., Orchard, P., Mahmoud, M., Paulin, L. F., Farek, J., Soto, D. C., Parker, S. C. J., Smith, A. V., Dennis, M. Y., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.18.500506 · Cited by 2
Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotypingPreprint
Peng, P. G. H., Lin, Y. H., Hajis, M. I. B., Maulana, Y., Hui, A. N. Q., Ramanto, K. N., Dewanggana, M. N., Irwanto, A. K., Sani, L. L., Liuh, L. G., et al. (2025) · medRxiv · doi:10.1101/2025.05.05.25326970 · Cited by 2
Segmental duplication-mediated rearrangements alter the landscape of mouse genomesPreprint
Francoeur, E. R., Audano, P. A., Ferraj, A., Balachandran, P., & Beck, C. R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.18.665526 · Cited by 2
Self-citation
Leaf: an ultrafast filter for population-scale long-read SV detection
Pan, C., & Reinert, K. (2024) · Genome biology · doi:10.1186/s13059-024-03297-5 · Cited by 1
Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes
Moosman, O. W., Kelley, J. L., & Bogan, S. N. (2025) · Heredity · doi:10.1038/s41437-025-00803-8 · Cited by 1
Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India
Joseph, J. S., Selvamani, S. B., Thiruvengadam, V., Ramasamy, G. G., Subramanian, S., Menon, G., Sivakumar, G., & Manjunath, C. (2025) · Molecular Biology Reports · doi:10.1007/s11033-025-11152-4 · Cited by 1
Unraveling the Genome of Epidendrum Fulgens : Demographic History and Gene Family Dynamics in a Resilient Neotropical Orchid
de Mattos, J. S., Aecyo, P., Keepers, K. G., Tavares, M. M., Rosa, F. D., Palma‐Silva, C., Kane, N. C., Pinheiro, F., & Riaño‐Pachón, D. M. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag057 · Cited by 1
Building and applying pangenome references to capture genetic diversity
Ashraf, H., Doerr, D., Ebler, J., & Marschall, T. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00987-7 · Cited by 1
Self-citation
Empowering rare variant burden-based gene-trait association studies via optimized computational predictor choicePreprint
Kuang, D., Li, R., Wu, Y., Weile, J., Hegele, R. A., & Roth, F. P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.09.20.459182 · Cited by 1
RAmbler: de novo genome assembly of complex repetitive regionsPreprint
Chakravarty, S., Logsdon, G. A., & Lonardi, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.26.542525 · Cited by 1
Hybrid-hybrid correction of errors in long reads with HEROPreprint
Kang, X., Xu, J., Luo, X. L., & Schönhuth, A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.11.10.566673 · Cited by 1
Human assemblies evaluated in the hifiasm paper
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H., & Li, H. (2020) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.4393630 · Cited by 1
Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigreesPreprint
Kramer, M., Goodwin, S., Wappel, R. L., Borio, M., Offit, K., Feldman, D. R., Stadler, Z. K., & McCombie, W. R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.27.601096 · Cited by 1
Bridging the gap: a prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxiaPreprint
Rafehi, H., Fearnley, L. G., Read, J. L., Snell, P., Davies, K. C., Scott, L. W., Gillies, G., Thompson, G. C., Field, T. A., Eldo, A., et al. (2024) · medRxiv · doi:10.1101/2024.07.08.24309939 · Cited by 1
Detecting and quantifying rare sex in natural populationsPreprint
Pieszko, T., Kelleher, J., Wilson, C. G., & Barraclough, T. G. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.03.657731 · Cited by 1
β 1 - and β 2 -adrenergic Receptor Haplotypes Regulate Therapeutic Responses to Placebo and the Biased Ligand β-blocker BucindololPreprint
Carroll, I. A., Slavov, D. B., Jonas, E. R., Minobe, W. A., Walker, L. A., Ambardekar, A. V., McKinsey, T. A., Knaupp, A. D., Kim, D., Liggett, S. B., et al. (2025) · medRxiv · doi:10.1101/2025.08.22.25333921 · Cited by 1
Faculty Opinions recommendation of Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Tang, F. (2021) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.739619698.793585652
Constructing founder sets under allelic and non-allelic homologous recombinationPreprint
Bonnet, K., Marschall, T., & Doerr, D. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.27.493721
Self-citation
Haplotype-resolved assemblies and variant benchmark of a Chinese QuartetPreprint
Jia, P., Dong, L., Yang, X., Wang, B., Wang, T., Lin, J., Wang, S., Zhao, X., Xu, T., Che, Y., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-2106421/v1
Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes
Hoehe, M. R., & Herwig, R. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2819-5_15
The telomere-to-telomere, gapless, phased diploid genome and methylome of the green alga Scenedesmus obliquus UTEX 3031 reveals significant heterozygosity and functional separation of the haplotypesPreprint
Biondi, T. C., Kruse, C. P. S., Koehler, S. I., Kwon, T., Eng, W., Kunde, Y. A., Gleasner, C. D., Mak, K. Y., Polle, J. E. W., Hovde, B. T., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.30.518549
Smaller, denser, smarter: improved Strand-seq library preparation, inversion genotyping, and phasing
Hanlon, V. C. T. (2023) · University of Groningen research database (University of Groningen / Centre for Information Technology) · doi:10.33612/diss.570000248
417. Expanding the cattle reference graph genome
Talenti, A., Powell, J., Wragg, D., Paxton, E. A., Chepkwony, M. C., Miyunga, A. A., Njeru, R., Hemmink, J. D., Fisch, A., Ferreira, B. R., et al. (2022) · World Congress on Genetics Applied to Livestock Production (WCGALP) · doi:10.3920/978-90-8686-940-4_417
Genome assembly of Parapercis colias (Blue cod/Rāwaru); An endemic marine fish species of New Zealand
Jackson, H. (2023) · Open Access Victoria University of Wellington | Te Herenga Waka (Figshare) · doi:10.26686/wgtn.24160266
Additional file 1 of Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Jia, P., Dong, L., Yang, X., Wang, B., Bush, S. J., Wang, T., Lin, J., Wang, S., Zhao, X., Xu, T., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24741805
Novel insight of the SVP gene involved in pedicel length based on genomics analysis in cherry
Tan, W., Zhou, P., Huang, X. S., Wang, Z., Liao, R., Hayat, F., Wang, X., Ni, Z., Shi, T., Yu, X., et al. (2025) · Plant Cell Reports · doi:10.1007/s00299-025-03439-4
Variations and Polymorphisms: The Human Pangenome Project
Pandey, S., Gambhir, S., Singh, V. K., & Bhardwaj, A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00184-6
Fully haplotyped genome assemblies of healthy individuals reveal variability in 5′ss strength and support by splicing regulatory proteins
Ptok, J., Theiss, S., & Schaal, H. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf036
Methods for Chromosome-Scale Haplotype Reconstruction
Garg, S. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4702-8_2
Life history and population biology
(2023) · CSIRO Publishing eBooks · doi:10.1071/9781486314935.bk08025_part2
Additional file 3 of Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data
Liu, Z., Xie, Z., & Li, M. (2024) · Figshare · doi:10.6084/m9.figshare.26749286
Additional file 3 of Inversion polymorphism in a complete human genome assembly
Porubskỳ, D., Harvey, W. T., Rozanski, A. N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A. D., Marschall, T., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724240
Self-citation
Additional file 4 of Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Jia, P., Dong, L., Yang, X., Wang, B., Bush, S. J., Wang, T., Lin, J., Wang, S., Zhao, X., Xu, T., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26649177
Additional file 1 of FixItFelix: improving genomic analysis by fixing reference errors
Behera, S., LeFaive, J., Orchard, P., Mahmoud, M., Paulin, L. F., Farek, J., Soto, D. C., Parker, S. C. J., Smith, A. V., Dennis, M. Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22612903
Additional file 3 of Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Jia, P., Dong, L., Yang, X., Wang, B., Bush, S. J., Wang, T., Lin, J., Wang, S., Zhao, X., Xu, T., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26649174
Additional file 1 of Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data
Liu, Z., Xie, Z., & Li, M. (2024) · Figshare · doi:10.6084/m9.figshare.26308976
Additional file 2 of Hybrid-hybrid correction of errors in long reads with HERO
Kang, X., Xu, J., Luo, X., & Schönhuth, A. (2024) · Figshare · doi:10.6084/m9.figshare.24715522
Additional file 5 of Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data
Liu, Z., Xie, Z., & Li, M. (2024) · Figshare · doi:10.6084/m9.figshare.26749292
Additional file 1 of Improving variant calling using population data and deep learning
Chen, N.-C., Kolesnikov, A., Goel, S., Yun, T., Chang, P.-C., & Carroll, A. W. (2023) · Figshare · doi:10.6084/m9.figshare.22815203
Additional file 2 of Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Jia, P., Dong, L., Yang, X., Wang, B., Bush, S. J., Wang, T., Lin, J., Wang, S., Zhao, X., Xu, T., et al. (2024) · Figshare · doi:10.6084/m9.figshare.24742937
Additional file 1 of Constructing founder sets under allelic and non-allelic homologous recombination
Bonnet, K., Marschall, T., & Doerr, D. (2024) · Figshare · doi:10.6084/m9.figshare.26621083
Self-citation
Additional file 5 of Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet
Jia, P., Dong, L., Yang, X., Wang, B., Bush, S. J., Wang, T., Lin, J., Wang, S., Zhao, X., Xu, T., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26649180
Additional file 4 of Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data
Liu, Z., Xie, Z., & Li, M. (2024) · Figshare · doi:10.6084/m9.figshare.26749289
Additional file 1 of Inversion polymorphism in a complete human genome assembly
Porubskỳ, D., Harvey, W. T., Rozanski, A. N., Ebler, J., Höps, W., Ashraf, H., Hasenfeld, P., Paten, B., Sanders, A. D., Marschall, T., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22724234
Self-citation
Additional file 1 of Hybrid-hybrid correction of errors in long reads with HERO
Kang, X., Xu, J., Luo, X., & Schönhuth, A. (2023) · Figshare · doi:10.6084/m9.figshare.24715430
Additional file 2 of Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data
Liu, Z., Xie, Z., & Li, M. (2024) · Figshare · doi:10.6084/m9.figshare.26309087
Additional file 3 of Hybrid-hybrid correction of errors in long reads with HERO
Kang, X., Xu, J., Luo, X., & Schönhuth, A. (2024) · Figshare · doi:10.6084/m9.figshare.26648136
Additional file 3 of FixItFelix: improving genomic analysis by fixing reference errors
Behera, S., LeFaive, J., Orchard, P., Mahmoud, M., Paulin, L. F., Farek, J., Soto, D. C., Parker, S. C. J., Smith, A. V., Dennis, M. Y., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22612909
Additional file 2 of Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
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.25034488
Self-citation

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
Publisher: Springer Science and Business Media LLC
Published: 2020-12-07
Volume: 39
Issue: 3
Pages: 302-308
ISSN: 0733-222X (ISSN-L)
1087-0156
1546-1696
DOI: 10.1038/s41587-020-0719-5
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
Licence: cc-by
creativecommons.org/licenses/by/4.0 (tdm)
creativecommons.org/licenses/by/4.0 (vor)
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

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks