Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph
Open accessAbstract
Despite advances in long-read sequencing technologies, constructing a near telomere-to-telomere assembly is still computationally demanding. Here we present hifiasm (UL), an efficient de novo assembly algorithm combining multiple sequencing technologies to scale up population-wide near telomere-to-telomere assemblies. Applied to 22 human and two plant genomes, our algorithm produces better diploid assemblies at a cost of an order of magnitude lower than existing methods, and it also works with polyploid genomes.
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These technological advancements led to a new generation of genome alignment and assembly algorithms leveraging new data types.
“These technological advancements also led to a new generation of genome alignment and assembly algorithms leveraging the new data types (84–89).”
From Topological Approaches in Animal Comparative Genomics (2026) · cites this paper as [85]
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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., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841 · see citing works
Self-citationA draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · cited 4× · see citing works
“To compare hifiasm (UL) with Verkko at a population scale, we evaluated both approaches using 22 human samples selected from the Human Pangenome Reference Consortium (HPRC) 13 .”
InfluentialSelf-citationThe design and construction of reference pangenome graphs with minigraph
Li, H., Feng, X., & Chu, C. (2020) · Genome Biology · doi:10.1186/s13059-020-02168-z · Cited by 455 · see citing works
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Research works printed but not linked: 11
- Cheng H, Concepcion GT, Feng X, Zhang H. & Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170-175 (2021). [PubMed: 33526886]
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Cited by
Sorted by citations
Topological Approaches in Animal Comparative Genomics
Schultz, D. T., & Simakov, O. (2026) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-030424-084541 · Cited by 1 · see citing works
- Authors
- Cheng, H., Asri, M., Lucas, J., Koren, S., & Li, H.
- Affiliations
- Harvard University (US)
- University of California, Santa Cruz (US)
- National Institutes of Health (US)
- Corresponding author
- Li, Heng
- Venue
- Nature Methods
- Published
- 2024-05-10
- Volume
- 21
- Issue
- 6
- Pages
- 967-970
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC11214949
- OpenAlex
- W4396803203
- Cited by
- 222
- References
- 3
- Citations by year
- 2026: 120 · 2025: 75 · 2024: 26 · 2023: 1
- FWCI
- 28.59
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- arXiv (Cornell University) (submittedVersion, cc-by)
- PubMed Central (submittedVersion, cc-by)
- arXiv (Cornell University) (cc-by)
- Funders
- U.S. Department of Health & Human Services | National Institutes of Health (R01HG010040, U01HG010971, U41HG010972, K99HG012798)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- telomere-to-telomere genome assembly, de novo genome assembly, Hifiasm, double graphs, polyploid genomes, diploid genome, long-read sequencing, PacBio HiFi, hybrid assembly
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