Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
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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.
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More than two-thirds of SVs have been missed in studies that used short-read data and the human reference assembly.
“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]
The Results section (‘Structural Variant Detection with CCS Reads’; page unavailable) shows that short-read calling missed structural variants, but its Manta callset had 55.88% recall—about 44% missed, not more than two-thirds. The comparison concerns a benchmark callset, not a finding about studies generally. (LLM, conf=0.85)
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- 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 · 2012: 1
- 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 ›
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