The DOI matches its Crossref record; 59 of the 59 references it cites were found in a registry or an index.
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
Open accessPublished version of a preprint
Abstract
The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.
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 source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“more than two-thirds of SVs have been missed in studies that used short-read data and the human reference assembly6–8”
From A draft human pangenome reference. (2023) · cites this paper as [7]
Experimental — accuracy not yet measuredIn the citing paper
“Recent technological advances by PacBio have enabled circular consensus sequencing of both RNA and DNA, resulting in long (>10 kb), highly accurate (99.8%) reads (136).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [136]
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
DNA sequencing with chain-terminating inhibitors
Sanger, F., Nicklen, S., & Coulson, A. R. (1977) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.74.12.5463 · Cited by 68,572
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
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
Self-citationThe sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Self-citationBUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344
A framework for variation discovery and genotyping using next-generation DNA sequencing data
DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457
Self-citationAnalysis of the genome sequence of the flowering plant Arabidopsis thaliana
Initiative, T. A. G. (2000) · Nature · doi:10.1038/35048692 · Cited by 9,301
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
Self-citationInitial sequencing and comparative analysis of the mouse genome
Mouse Genome Sequencing Consortium (2002) · Nature · doi:10.1038/nature01262 · Cited by 7,187
Cited by
Sorted by citations
Items 301–400 of 1,001
Jousheghani, Z. Z., Singh, N., & Patro, R. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf240 · Cited by 48
Kingan, S. B., Urban, J., Lambert, C. C., Baybayan, P. A., Childers, A. K., Coates, B. S., Scheffler, B. E., Hackett, K. J., Korlach, J., & Geib, S. M. (2019) · GigaScience · doi:10.1093/gigascience/giz122 · Cited by 45
phasebook: haplotype-aware de novo assembly of diploid genomes from long reads
Luo, X. L., Kang, X., & Schönhuth, A. (2021) · Genome biology · doi:10.1186/s13059-021-02512-x · Cited by 43
Analysis of rare thalassemia genetic variants based on third-generation sequencing
Peng, C., Zhang, H., Ren, J., Chen, H., Du, Z., Zhao, T., Mao, A., Xu, R., Lu, Y., Wang, H., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-14038-8 · Cited by 44
RNA recoding in cephalopods tailors microtubule motor protein function
Rangan, K. J., & Reck‐Peterson, S. L. (2023) · Cell · doi:10.1016/j.cell.2023.04.032 · Cited by 46
vamos: variable-number tandem repeats annotation using efficient motif sets
Ren, J., Gu, B., & Chaisson, M. (2023) · Genome biology · doi:10.1186/s13059-023-03010-y · Cited by 41
Luan, T., Commichaux, S., Hoffmann, M., Jayeola, V., Jang, J. H., Pop, M., Rand, H. A., & Luo, Y. (2024) · BMC Genomics · doi:10.1186/s12864-024-10582-x · Cited by 49
Toward clinical long-read genome sequencing for rare diseases
Eisfeldt, J., Ek, M., Nordenskjöld, M., & Lindstrand, A. (2025) · Nature Genetics · doi:10.1038/s41588-025-02160-y · Cited by 47
Breeding Intermediate Wheatgrass for Grain Production
Bajgain, P., Crain, J. L., Cattani, D. J., Larson, S. R., Altendorf, K. R., Anderson, J. A., Crews, T. E., Hu, Y., Poland, J., Turner, M. K., et al. (2022) · Plant breeding reviews · doi:10.1002/9781119874157.ch3 · Cited by 46
Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., et al. (2023) · Genome Research · doi:10.1101/gr.277481.122 · Cited by 43
Variant calling: Considerations, practices, and developments
Zverinova, S., & Guryev, V. (2021) · Human Mutation · doi:10.1002/humu.24311 · Cited by 49
Fish Genomics and Its Application in Disease‐Resistance Breeding
Huang, Y. S., Li, Z., Li, M., Zhang, X., Shi, Q., & Xu, Z. (2024) · Reviews in Aquaculture · doi:10.1111/raq.12973 · Cited by 46
SequelTools: a suite of tools for working with PacBio Sequel raw sequence data
Hufnagel, D. E., Hufford, M. B., & Seetharam, A. S. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03751-8 · Cited by 43
Ko, S. H., Mokhtari, E. B., Mudvari, P., Stein, S. R., Stringham, C. D., Wagner, D. A., Ramelli, S. C., Ramos-Benítez, M. J., Strich, J. R., Davey, R. T., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009431 · Cited by 41
Application of long-read sequencing to the detection of structural variants in human cancer genomes
Sakamoto, Y., Zaha, S., Suzuki, Y., Seki, M., & Suzuki, A. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.07.030 · Cited by 41
Representing sex chromosomes in genome assemblies
Carey, S. B., Lovell, J. T., Jenkins, J. W., Leebens‐Mack, J., Schmutz, J., Wilson, M. A., & Harkess, A. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100132 · Cited by 40
Nakandala, U., Masouleh, A. K., Smith, M. W., Furtado, A., Mason, P. J., Constantin, L., & Henry, R. J. (2023) · Horticulture Research · doi:10.1093/hr/uhad058 · Cited by 40
HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing
Holt, J., Saunders, C. T., Rowell, W. J., Kronenberg, Z. N., Wenger, A. M., & Eberle, M. A. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae042 · Cited by 42
Self-citationCurrent Analytical Strategies for mRNA-Based Therapeutics
Camperi, J., Chatla, K., Freund, E. C., Galan, C., Lippold, S., & Guilbaud, A. (2025) · Molecules · doi:10.3390/molecules30071629 · Cited by 47
Rapid and ongoing evolution of repetitive sequence structures in human centromeres
Suzuki, Y., Myers, E. W., & Morishita, S. (2020) · Science Advances · doi:10.1126/sciadv.abd9230 · Cited by 42
Cosentino, R. O., Brink, B. G., & Siegel, T. N. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab082 · Cited by 40
Harvey, W. T., Ebert, P., Ebler, J., Audano, P. A., Munson, K. M., Hoekzema, K., Porubskỳ, D., Beck, C. R., Marschall, T., Garimella, K. V., et al. (2023) · Genome Research · doi:10.1101/gr.278070.123 · Cited by 43
Self-citationIntegrated analysis of the complete sequence of a macaque genome
Zhang, S., Xu, N., Fu, L., Yang, X., Ma, K., Li, Y., Yang, Z., Li, Z., Feng, Y., Jiang, X., et al. (2025) · Nature · doi:10.1038/s41586-025-08596-w · Cited by 48
Self-citationHigh-Level Acquisition of Maternal Oral Bacteria in Formula-Fed Infant Oral Microbiota
Kageyama, S., Furuta, M., Takeshita, T., Ma, J., Asakawa, M., & Yamashita, Y. (2022) · mBio · doi:10.1128/mbio.03452-21 · Cited by 44
Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species
Fernandez, C. G. T., Nestor, B. J., Danilevicz, M. F., Gill, M., Petereit, J., Bayer, P. E., Finnegan, P. M., Batley, J., & Edwards, D. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23052671 · Cited by 43
Structural polymorphism and diversity of human segmental duplications
Jeong, H., Dishuck, P. C., Yoo, D., Harvey, W. T., Munson, K. M., Lewis, A. P., Kordosky, J., Garcia, G. H., Yilmaz, F., Hallast, P., et al. (2025) · Nature Genetics · doi:10.1038/s41588-024-02051-8 · Cited by 47
Sabatella, M., Mantere, T., Waanders, E., Neveling, K., Mensenkamp, A. R., van Dijk, F., Hehir‐Kwa, J. Y., Derks, R., Kwint, M. P., O’Gorman, L., et al. (2021) · The Journal of Pathology · doi:10.1002/path.5755 · Cited by 41
Wong, L. L., Razali, S. A., Deris, Z. M., Danish‐Daniel, M., Tan, M. P., Nor, S. A. M., Ma, H., Min, W., Yantao, L., Asaduzzaman, M., et al. (2021) · Aquaculture · doi:10.1016/j.aquaculture.2021.737633 · Cited by 40
Jiang, T., Liu, S., Cao, S., Liu, Y., Cui, Z., Wang, Y., & Guo, H. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04422-y · Cited by 39
Stevens, L., Moya, N. D., Tanny, R. E., Gibson, S. B., Tracey, A., Na, H., Zhan, Y., Chitrakar, R., Dekker, J., Walhout, A. J. M., et al. (2022) · Genome Biology and Evolution · doi:10.1093/gbe/evac042 · Cited by 40
Orellana, L. H., Krüger, K., Sidhu, C., & Amann, R. (2023) · Microbiome · doi:10.1186/s40168-023-01557-3 · Cited by 40
Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology
Han, Y., He, J., Li, M., Peng, Y., Jiang, H., Zhao, J., Li, Y., & Deng, F. (2024) · Microorganisms · doi:10.3390/microorganisms12122482 · Cited by 43
Isaic, A., Motofelea, N., Hoinoiu, T., Motofelea, A. C., Leancu, I. C., Stan, E., Gheorghe, S. R., Duţu, A., & Crintea, A. (2025) · Diagnostics · doi:10.3390/diagnostics15192425 · Cited by 50
State-of-the-art genome inference in the human MHC
Dilthey, A. (2020) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2020.105882 · Cited by 42
Artesi, M., Hahaut, V., Cole, B., Lambrechts, L., Ashrafi, F., Marçais, A., Hermine, O., Griebel, P. J., Arsic, N., van der Meer, F. J. U. M., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02307-0 · Cited by 45
Using de novo assembly to identify structural variation of eight complex immune system gene regions
Zhang, J., Roberts, H., Cruz, D. F. S., Cutler, A. J., Brown, A., Whalley, J. P., Mielczarek, O., Buck, D., Lockstone, H. E., Xella, B., et al. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009254 · Cited by 40
Haro-Moreno, J. M., López‐Pérez, M., & Rodríguez‐Valera, F. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.708782 · Cited by 40
Driguez, P., Bougouffa, S., Carty, K., Putra, A., Jabbari, K., Reddy, M., Soppe, R. W. O., Cheung, M. S., Fukasawa, Y., & Ermini, L. (2021) · Genome biology · doi:10.1186/s13059-021-02475-z · Cited by 38
Fukuda, H., Yamaguchi, D., Nyquist, K., Yabuki, Y., Miyatake, S., Uchiyama, Y., Hamanaka, K., Saida, K., Koshimizu, E., Tsuchida, N., et al. (2021) · Clinical Epigenetics · doi:10.1186/s13148-021-01192-5 · Cited by 42
Self-citationLessons learned: next-generation sequencing applied to undiagnosed genetic diseases
Schuler, B. A., Nelson, E. T., Koziura, M. E., Cogan, J. D., Hamid, R., & Phillips, J. A. (2022) · Journal of Clinical Investigation · doi:10.1172/jci154942 · Cited by 41
Li, X., Mank, J. E., & Ban, L. (2024) · Genome Research · doi:10.1101/gr.278794.123 · Cited by 42
HiCAT: a tool for automatic annotation of centromere structure
Gao, S., Yang, X., Guo, H., Zhao, X., Wang, B., & Ye, K. (2023) · Genome biology · doi:10.1186/s13059-023-02900-5 · Cited by 39
Lager-brewing yeasts in the era of modern genetics
de Vries, A. R. G., Pronk, J. T., & Daran, J.-M. G. (2019) · FEMS Yeast Research · doi:10.1093/femsyr/foz063 · Cited by 41
Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities
Minervini, C. F., Cumbo, C., Orsini, P., Anelli, L., Zagaria, A., Specchia, G., & Albano, F. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00076 · Cited by 40
The additional diagnostic yield of long-read sequencing in undiagnosed rare diseasesPreprint
Gobbo, G. F. D., & Boycott, K. M. (2025) · Genome Research · doi:10.1101/gr.279970.124 · Cited by 44
Udaondo, Z., Sittikankaew, K., Uengwetwanit, T., Wongsurawat, T., Sonthirod, C., Jenjaroenpun, P., Pootakham, W., Karoonuthaisiri, N., & Nookaew, I. (2021) · Life · doi:10.3390/life11080862 · Cited by 38
The genetic landscape and phenotypic spectrum of GAA-FGF14 ataxia in China: a large cohort study
Ouyang, R., Wan, L., Pellerin, D., Long, Z., Hu, J. M., Jiang, Q., Wang, C., Peng, L., Peng, H., He, L., et al. (2024) · EBioMedicine · doi:10.1016/j.ebiom.2024.105077 · Cited by 36
van der Lee, M., Rowell, W. J., Menafra, R., Guchelaar, H., Swen, J. J., & Anvar, S. Y. (2021) · The Pharmacogenomics Journal · doi:10.1038/s41397-021-00259-z · Cited by 38
Self-citationCharnaud, S. C., Munro, J. E., Semenec, L., Mazhari, R., Brewster, J., Bourke, C., Ruybal‐Pesántez, S., James, R. S., Lautu‐Gumal, D., Karunajeewa, H., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03102-8 · Cited by 37
Brown, T., Mishra, K., Elewa, A., Iarovenko, S. I., Subramanian, E., Joven, A., Petzold, A., Fromm, B., Friedländer, M. R., Rikk, L., et al. (2025) · Cell Genomics · doi:10.1016/j.xgen.2025.100761 · Cited by 39
Potential of Whole-Genome Sequencing-Based Pharmacogenetic Profiling
Caspar, S. M., Schneider, T., Stoll, P., Meienberg, J., & Mátyás, G. (2021) · Pharmacogenomics · doi:10.2217/pgs-2020-0155 · Cited by 37
Rasekh, M. E., Hernandez, Y. A., Drinan, S. D., Bass, J. I. F., & Benson, G. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab224 · Cited by 37
Petersen, C., Sørensen, T., Westphal, K. R., Fechete, L. I., Søndergaard, T. E., Sørensen, J. L., & Nielsen, K. L. (2022) · Microbial Genomics · doi:10.1099/mgen.0.000816 · Cited by 36
From genome structure to function: insights into structural variation in microbiology
West, P. T., Chanin, R. B., & Bhatt, A. S. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102192 · Cited by 36
Kumar, V., Kumar, P., Bhargava, B., Sharma, R., Irfan, M., & Chandora, R. (2023) · Journal of Plant Growth Regulation · doi:10.1007/s00344-023-11018-8 · Cited by 36
Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics
Su, T., Hollas, M. A. R., Fellers, R. T., & Kelleher, N. L. (2023) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-020722-044021 · Cited by 40
Genomic variant benchmark: if you cannot measure it, you cannot improve it
Majidian, S., Agustinho, D. P., Chin, C.-S., Sedlazeck, F. J., & Mahmoud, M. (2023) · Genome biology · doi:10.1186/s13059-023-03061-1 · Cited by 35
Self-citationReference Materials for Improving Reliability of Multiomics Profiling
Ren, L., Shi, L. M., & Zheng, Y. (2024) · Phenomics · doi:10.1007/s43657-023-00153-7 · Cited by 37
The single-molecule accessibility landscape of newly replicated mammalian chromatin
Ostrowski, M. S., Yang, M. G., McNally, C. P., Abdulhay, N. J., Wang, S., Renduchintala, K., Irkliyenko, I., Biran, A., Chew, B. T. L., Midha, A. D., et al. (2024) · Cell · doi:10.1016/j.cell.2024.10.039 · Cited by 35
PacBio sequencing output increased through uniform and directional fivefold concatenation
Kanwar, N., Blanco, C., Chen, I. A., & Seelig, B. (2021) · Scientific Reports · doi:10.1038/s41598-021-96829-z · Cited by 38
Culturing the uncultured microbial majority in activated sludge: A critical review
Zhang, Y., & Zhang, T. (2022) · Critical Reviews in Environmental Science and Technology · doi:10.1080/10643389.2022.2077063 · Cited by 38
Martinez‐Hernández, F., Diop, A., García-Heredia, I., Bobay, L., & Martínez‐García, M. (2021) · The ISME Journal · doi:10.1038/s41396-021-01150-2 · Cited by 35
Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine
Geo, J. A., Ameen, R. M., Alshemmari, S., & Thomas, J. P. (2024) · Medical Principles and Practice · doi:10.1159/000538176 · Cited by 36
De novo diploid genome assembly using long noisy reads
Nie, F., Ni, P., Huang, N., Zhang, J., Wang, Z., Xiao, C., Luo, F., & Wang, J. (2024) · Nature Communications · doi:10.1038/s41467-024-47349-7 · Cited by 37
LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads
Jam, H. Z., Zook, J. M., Javadzadeh, S., Park, J., Sehgal, A., & Gymrek, M. (2024) · Genome biology · doi:10.1186/s13059-024-03319-2 · Cited by 40
Self-citationArtificial intelligence in variant calling: a review
Abdelwahab, O., & Torkamaneh, D. (2025) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2025.1574359 · Cited by 45
Allio, R., Tilak, M., Scornavacca, C., Avenant, N. L., Kitchener, A. C., Corre, E., Nabholz, B., & Delsuc, F. (2021) · eLife · doi:10.7554/elife.63167 · Cited by 38
Expression level is a major modifier of the fitness landscape of a protein coding gene
Wu, Z., Cai, X., Zhang, X., Liu, Y., Tian, G., Yang, J., & Chen, X. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01578-x · Cited by 32
Long-Reads-Based Metagenomics in Clinical Diagnosis With a Special Focus on Fungal Infections
Hoang, M. T. V., Irinyi, L., Hu, Y., Schwessinger, B., & Meyer, W. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.708550 · Cited by 35
Wu, H.-Y., & Shaw, P. (2022) · Chinese Medicine · doi:10.1186/s13020-022-00590-y · Cited by 38
Chen, J., Cheng, J., Chen, X., Inoue, M., Liu, Y., & Song, C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac612 · Cited by 37
Lavrichenko, K., Johansson, S., & Jonassen, I. (2021) · BMC Genomics · doi:10.1186/s12864-021-08082-3 · Cited by 36
Phasing analysis of lung cancer genomes using a long read sequencer
Sakamoto, Y., Miyake, S., Oka, M., Kanai, A., Kawai, Y., Nagasawa, S., Shiraishi, Y., Tokunaga, K., Kohno, T., Seki, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31133-6 · Cited by 31
A chromosome-level reference genome and pangenome for barn swallow population genomics
Secomandi, S., Gallo, G. R., Sozzoni, M., Iannucci, A., Galati, E., Abueg, L. A. L., Balacco, J., Caprioli, M., Chow, W., Ciofi, C., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.111992 · Cited by 37
Self-citationBaker, J. L. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad051 · Cited by 37
A head-to-head NLR gene pair from wild emmer confers stripe rust resistance in wheat
Hu, Y., Li, M., Li, Y., Du, L., Xie, R., Ni, F., Xia, C., Wang, K., Huang, Y., Xu, B., et al. (2025) · Nature Genetics · doi:10.1038/s41588-025-02207-0 · Cited by 39
Huang, C.-K., Lin, W., & Wu, S. (2022) · Genome biology · doi:10.1186/s13059-022-02620-2 · Cited by 33
Complex genome assembly based on long-read sequencing
Zhang, T., Zhou, J., Gao, W., Jia, Y., Wei, Y., & Wang, G. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac305 · Cited by 38
Akbari, V., Hanlon, V. C. T., O’Neill, K., Lefebvre, L., Schrader, K. A., Lansdorp, P. M., & Jones, S. J. M. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100233 · Cited by 33
Gueuning, M., Thun, G. A., Wittig, M., Galati, A.-L., Meyer, S., Trost, N., Gourri, E., Fuß, J., Sigurdardottir, S., Merki, Y., et al. (2022) · Blood Advances · doi:10.1182/bloodadvances.2022007133 · Cited by 32
The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing
Foord, C., Hsu, J., Jarroux, J., Hu, W., Belchikov, N., Pollard, S., He, Y., Joglekar, A., & Tilgner, H. (2023) · Nature Methods · doi:10.1038/s41592-022-01715-9 · Cited by 31
Li, C.-C., Hsu, W.-F., Chiang, P.-C., Kuo, M., Wo, A. M., & Tseng, Y. J. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2288200 · Cited by 33
Helal, A. A., Saad, B. T., Saad, M. T., Mosaad, G. S., & Aboshanab, K. M. (2024) · Scientific Reports · doi:10.1038/s41598-024-56604-2 · Cited by 35
Rosaceae phylogenomic studies provide insights into the evolution of new genes
Jiang, L., Li, X., Lyu, K., Wang, H., Li, Z., Qi, W., Zhang, L., & Cao, Y. (2024) · Horticultural Plant Journal · doi:10.1016/j.hpj.2024.02.002 · Cited by 35
Exploring gene content with pangene graphs
Li, H., Marin, M. G., & Farhat, M. R. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae456 · Cited by 37
Self-citationFrampton, S., Smith, R., Ferson, L., Gibson, J., Hollox, E. J., Cragg, M. S., & Strefford, J. C. (2024) · Immunological Reviews · doi:10.1111/imr.13401 · Cited by 37
Saunders, C. T., Holt, J., Baker, D. N., Lake, J. A., Belyeu, J. R., Kronenberg, Z. N., Rowell, W. J., & Eberle, M. A. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf136 · Cited by 35
Self-citationCross, B. J., Partridge, S. R., & Sheppard, A. E. (2025) · Microbiological Research · doi:10.1016/j.micres.2025.128340 · Cited by 33
Zaghum, M. J., Ali, K., & Teng, S. (2022) · Agriculture · doi:10.3390/agriculture12111757 · Cited by 33
Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers
Wei, A., & Wu, H. (2022) · Development · doi:10.1242/dev.182683 · Cited by 34
Sequencing and Assembly of Polyploid Genomes
Wang, Y., Yu, J., Jiang, M., Lei, W., Zhang, X., & Tang, H. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-2561-3_23 · Cited by 34
Distinct regulatory functions and biological roles of lncRNA splice variants
Khan, M. R., Avino, M., Wellinger, R. J., & Laurent, B. (2023) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2023.03.004 · Cited by 34
Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomesPreprint
Yu, W., Luo, H., Yang, J., Zhang, S., Jiang, H., Zhao, X., Hui, X., Sun, D., Li, L., Wei, X.-Q., et al. (2024) · Genome Research · doi:10.1101/gr.278232.123 · Cited by 34
DeepTrio: Variant Calling in Families Using Deep Learning
Brambrink, L., Kolesnikov, A., Goel, S., Nattestad, M., Yun, T., Baid, G., Yang, H., McLean, C., Shafin, K., Chang, P.-C., et al. (2021) · doi:10.1101/2021.04.05.438434 · Cited by 32
Self-citationWestfall, D. H., Deng, W., Pankow, A. P., Murrell, H., Chen, L., Zhao, H. C., Williamson, C. E., Rolland, M., Murrell, B., & Mullins, J. I. (2024) · Virus Evolution · doi:10.1093/ve/veae019 · Cited by 31
Olagunju, T., Rosen, B. D., Neibergs, H. L., Becker, G. M., Davenport, K. M., Elsik, C. G., Hadfield, T. S., Koren, S., Kuhn, K. L., Rhie, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52384-5 · Cited by 36
Self-citationHum, M., & Lee, A. S. G. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-06495-2 · Cited by 35
Probabilistic Estimation of Identity by Descent Segment Endpoints and Detection of Recent Selection
Browning, S. R., & Browning, B. L. (2020) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2020.09.010 · Cited by 34
Okada, E., Morisada, N., Horinouchi, T., Fujii, H., Tsuji, T., Miura, M., Katori, H., Kitagawa, M., Morozumi, K., Toriyama, T., et al. (2022) · Kidney International Reports · doi:10.1016/j.ekir.2021.12.037 · Cited by 32
Structural Variant Detection from Long-Read Sequencing Data with cuteSV
Jiang, T., Liu, S., Cao, S., & Wang, Y. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2293-3_9 · Cited by 30
Metadata
- Authors
- Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., Töpfer, A., Alonge, M., Mahmoud, M., Qian, Y., Chin, C.-S., Phillippy, A. M., Schatz, M. C., Myers, G., DePristo, M. A., Ruan, J., Marschall, T., Sedlazeck, F. J., Zook, J. M., Li, H., Koren, S., Carroll, A., Rank, D. R., & Hunkapiller, M. W.
- Affiliations
- Pacific Biosciences (United States) (US)
- Google (United States) (US)
- Max Planck Institute for Informatics (DE)
- DNAnexus (United States) (US)
- National Institute of Standards and Technology (US)
- Johns Hopkins University (US)
- Baylor College of Medicine (US)
- National Institutes of Health (US)
- Agricultural Genomics Institute at Shenzhen (CN)
- Dana-Farber Cancer Institute (US)
- Corresponding author
- Rank, David R.
- Hunkapiller, Michael W.
- ORCID
- Wenger, Aaron M.
- Peluso, Paul
- Rowell, William J.
- Chang, Pi-Chuan
- Hall, Richard J.
- Concepcion, Gregory T.
- Ebler, Jana
- Fungtammasan, Arkarachai
- Kolesnikov, Alexey
- Olson, Nathan D.
- Töpfer, Armin
- Alonge, Michael
- Mahmoud, Medhat
- Chin, Chen-Shan
- Phillippy, Adam M.
- Schatz, Michael C.
- DePristo, Mark A.
- Ruan, Jue
- Marschall, Tobias
- Sedlazeck, Fritz J.
- Zook, Justin M.
- Li, Heng
- Koren, Sergey
- Carroll, Andrew
- Rank, David R.
- Hunkapiller, Michael W.
- Venue
- Nature Biotechnology
- Published
- 2019-08-12
- Volume
- 37
- Issue
- 10
- Pages
- 1155-1162
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC6776680
- OpenAlex
- W2968499116
- Cited by
- 1,841
- References
- 57
- Citations by year
- 2026: 246 · 2025: 300 · 2024: 326 · 2023: 275 · 2022: 261 · 2021: 241 · 2020: 133 · 2019: 56
- FWCI
- 60.58
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Biotechnology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Deutsche Forschungsgemeinschaft (391137747, 395192176)
- National Science Foundation (DBI-1350041)
- U.S. Department of Health & Human Services | National Institutes of Health (R01-HG006677, UM1 HG008898, 1R01HG010040)
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute
- National Natural Science Foundation of China (31571353, 31822029)
- 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 › Genetics › Genomics and Rare Diseases
- Keywords
- circular consensus sequencing, single-molecule real-time sequencing, PacBio HiFi reads, variant calling, structural variants, indels, single nucleotide variants, haplotype phasing, de novo genome assembly
- MeSH terms
- Base Sequence, DNA, Circular, Haplotypes, Humans, Genetic Variation, Genome, Human, Sequence Analysis, DNA, 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
