Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Open accessAbstract
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully represent the haplotype information in a phased assembly graph. Unlike other graph-based assemblers that only aim to maintain the contiguity of one haplotype, hifiasm strives to preserve the contiguity of all haplotypes. This feature enables the development of a graph trio binning algorithm that greatly advances over standard trio binning. On three human and five nonhuman datasets, including California redwood with a ~30-Gb hexaploid genome, we show that hifiasm frequently delivers better assemblies than existing tools and consistently outperforms others on haplotype-resolved assembly.
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
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 HiFi depth of coverage is consistent with the requirements for high-quality, state-of-the-art assemblies and facilitates comprehensive variant discovery irrespective of allele frequency.
“This depth of coverage is consistent with the requirements for high-quality, state-of-the-art assemblies20 and facilitates comprehensive variant discovery irrespective of allele frequency (AF).”
From A draft human pangenome reference. (2023) · cites this paper as [20]
The Discussion reports that hifiasm produces high-quality haplotype-resolved assemblies from HiFi reads, supporting the assembly-quality portion of the citation. The passages on coverage in the Online Methods do not establish that the citing document’s depth meets a specified coverage requirement. The citation is attached to the assembly clause; the paper also does not establish variant discovery irrespective of allele frequency. (LLM, conf=0.79)
Experimental — accuracy not yet measuredThe authors chose Trio-Hifiasm as the core assembler after detailed benchmarking of several alternatives.
“For the core assembler, we chose Trio-Hifiasm20 after detailed benchmarking of several alternatives21.”
From A draft human pangenome reference. (2023) · cites this paper as [20]
These improvements are the result of recent improvements in de novo assembly driven by better sequencing technology and coordinated innovations in assembly algorithms.
“These improvements are the result of recent improvements in de novo assembly driven both by better sequencing technology and coordinated innovations in assembly algorithms20,21.”
From A draft human pangenome reference. (2023) · cites this paper as [20]
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 [84]
Yak k-mer analyser estimated an average quality value of 53.57 for the assemblies, corresponding to an average of 1 base error per 227,509 bases.
“Using short substrings (k-mer values of 31) derived from Illumina data, the Yak k-mer analyser20 estimated an average quality value (QV) of 53.57 for the assemblies, which corresponded to an average of 1 base error per 227,509 bases (Fig. 1e).”
From A draft human pangenome reference. (2023) · cites this paper as [20]
The cited paper’s Results discuss hifiasm assembly quality, but the passages in our copy do not identify the Yak k-mer analyser or report a QV of 53.57 or one error per 227,509 bases. Searches for Yak and those figures found no passage addressing the cited measurement. (LLM, conf=0.76)
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.
Cites
Minimap2: Pairwise alignment for nucleotide sequences
Li, H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty191 · Cited by 14,807 · see citing works
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 · see citing works
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172 · see citing works
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 7,340 · see citing works
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 · see citing works
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chin, C., Alexander, D., Marks, P., Klammer, A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,008 · see citing works
Identifying and removing haplotypic duplication in primary genome assemblies
Guan, D., McCarthy, S., Wood, J. M. D., Howe, K., Wang, Y., & Durbin, R. M. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa025 · Cited by 2,728 · see citing works
Phased diploid genome assembly with single-molecule real-time sequencing
Chin, C.-S., Peluso, P. S., Sedlazeck, F. J., Nattestad, M., Concepcion, G. T., Clum, A., Dunn, C., O’Malley, R. C., Figueroa-Balderas, R. E., Morales‐Cruz, A., et al. (2016) · Nature Methods · doi:10.1038/nmeth.4035 · Cited by 1,847 · see citing works
Self-citationWenger, 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-citationMinimap and miniasm: fast mapping and de novo assembly for noisy long sequences
Li, H. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw152 · Cited by 1,460 · see citing works
Self-citationFast and accurate long-read assembly with wtdbg2
Ruan, J., & Li, H. (2019) · Nature Methods · doi:10.1038/s41592-019-0669-3 · Cited by 1,314 · see citing works
Self-citationAssembling large genomes with single-molecule sequencing and locality-sensitive hashing
Berlin, K., Koren, S., Chin, C.-S., Drake, J. P., Landolin, J. M., & Phillippy, A. M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3238 · Cited by 928 · see citing works
Multi-platform discovery of haplotype-resolved structural variation in human genomes
Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-08148-z · Cited by 891 · see citing works
Nurk, S., Walenz, B. P., Rhie, A., Vollger, M. R., Logsdon, G. A., Grothe, R., Miga, K. H., Eichler, E. E., Phillippy, A. M., & Koren, S. (2020) · Genome Research · doi:10.1101/gr.263566.120 · Cited by 709 · see citing works
Origin and evolution of the octoploid strawberry genome
Edger, P. P., Poorten, T. J., VanBuren, R., Hardigan, M. A., Colle, M., McKain, M. R., Smith, R. D., Teresi, S. J., Nelson, A. D. L., Wai, C. M., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0356-4 · Cited by 685 · see citing works
Aggressive assembly of pyrosequencing reads with mates
Miller, J. R., Delcher, A. L., Koren, S., Venter, E., Walenz, B. P., Brownley, A., Johnson, J. H., Li, K., Mobarry, C. M., & Sutton, G. G. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn548 · Cited by 604 · see citing works
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes
Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0503-6 · Cited by 567 · see citing works
De novo assembly of haplotype-resolved genomes with trio binning
Koren, S., Rhie, A., Walenz, B. P., Dilthey, A., Bickhart, D. M., Kingan, S. B., Hiendleder, S., Williams, J. L., Smith, T. P. L., & Phillippy, A. M. (2018) · Nature Biotechnology · doi:10.1038/nbt.4277 · Cited by 494 · see citing works
A fast bit-vector algorithm for approximate string matching based on dynamic programming
Myers, G. (1999) · Journal of the ACM · doi:10.1145/316542.316550 · Cited by 461 · see citing works
The 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
Self-citationWhatsHap: fast and accurate read-based phasingPreprint
Martin, M., Patterson, M., Garg, S., Fischer, S. O., Pisanti, N., Klau, G. W., Schönhuth, A., & Marschall, T. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/085050 · Cited by 454 · see citing works
Efficient assembly of nanopore reads via highly accurate and intact error correction
Chen, Y., Nie, F., Xie, S., Zheng, Y., Dai, Q., Bray, T., Wang, Y.-X., Xing, J.-F., Huang, Z., Wang, D., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20236-7 · Cited by 430 · see citing works
The fragment assembly string graph
Myers, E. W. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1114 · Cited by 424 · see citing works
An open resource for accurately benchmarking small variant and reference calls
Zook, J. M., McDaniel, J., Olson, N. D., Wagner, J., Parikh, H. M., Heaton, H., Irvine, S. A., Trigg, L., Truty, R., McLean, C. Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0074-6 · Cited by 404 · see citing works
Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly
Li, H. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts280 · Cited by 398 · see citing works
Self-citationHapCUT2: robust and accurate haplotype assembly for diverse sequencing technologiesPreprint
Edge, P., Bafna, V., & Bansal, V. (2016) · Genome Research · doi:10.1101/gr.213462.116 · Cited by 379 · see citing works
Highly accurate long-read HiFi sequencing data for five complex genomes
Hon, T., Mars, K., Young, G., Tsai, Y., Karalius, J. W., Landolin, J. M., Maurer, N. W., Kudrna, D. A., Hardigan, M. A., Steiner, C., et al. (2020) · Scientific Data · doi:10.1038/s41597-020-00743-4 · Cited by 349 · see citing works
A synthetic-diploid benchmark for accurate variant-calling evaluation
Li, H., Bloom, J. M., Farjoun, Y., Fleharty, M., Gauthier, L. D., Neale, B. M., & MacArthur, D. G. (2018) · Nature Methods · doi:10.1038/s41592-018-0054-7 · Cited by 231 · see citing works
Self-citationCleary, J. G., Braithwaite, R., Gaastra, K., Hilbush, B. S., Inglis, S., Irvine, S. A., Jackson, A., Littin, R., Rathod, M., Ware, D., et al. (2015) · doi:10.1101/023754 · Cited by 230 · see citing works
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., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0719-5 · Cited by 203 · see citing works
Chromosome-scale, haplotype-resolved assembly of human genomes
Garg, S., Fungtammasan, A., Carroll, A. W., Chou, M., Schmitt, A. D., Zhou, X., Mac, S., Peluso, P. S., Hatas, E., Ghurye, J., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0711-0 · Cited by 177 · see citing works
Self-citationMulti-platform discovery of haplotype-resolved structural variation in human genomesPreprint
Chaisson, M., Sanders, A. D., Zhao, X., Malhotra, A., Porubskỳ, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/193144 · Cited by 145 · see citing works
Human Genome Assembly in 100 MinutesPreprint
Chin, C.-S., & Khalak, A. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/705616 · Cited by 97 · see citing works
Nurk, S., Walenz, B. P., Rhie, A., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.14.992248 · Cited by 96 · see citing works
A diploid assembly-based benchmark for variants in the major histocompatibility complex
Chin, C.-S., Wagner, J., Zeng, Q., Garrison, E., Garg, S., Fungtammasan, A., Rautiainen, M., Aganezov, S., Kirsche, M., Zarate, S., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18564-9 · Cited by 82 · see citing works
Hizume, M., Kondo, T., Shibata, F., et al. (2001) · CYTOLOGIA · doi:10.1508/cytologia.66.307 · Cited by 78 · see citing works
Identifying and removing haplotypic duplication in primary genome assembliesPreprint
Guan, D., McCarthy, S., Wood, J. M. D., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/729962 · Cited by 71 · see citing works
Highly accurate long-read HiFi sequencing data for five complex genomesPreprint
Hon, T., Mars, K., Young, G., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.04.077180 · Cited by 49 · see citing works
BitMapper: an efficient all-mapper based on bit-vector computing
Cheng, H., Jiang, H., Yang, J., et al. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0626-9 · Cited by 38 · see citing works
Self-citationA Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility ComplexPreprint
Chin, C.-S., Wagner, J., Zeng, Q., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/831792 · Cited by 20 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [9]Chen Y Fast and accurate assembly of Nanopore reads via progressive error correction and adaptive read selection. Preprint at bioRxiv https://www.biorxiv.org/content/10.1101/2020.02.01.930107v1 (2020). · DOI
Cited by
Sorted by citations
The complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136 · 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 · see citing works
“Trio-Hifiasm uses PacBio HiFi long-reads and parental Illumina short-reads to produce near fully phased contig assemblies.”
BackgroundMethodInfluentialSelf-citationHaplotype-resolved diverse human genomes and integrated analysis of structural variation
Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science · doi:10.1126/science.abf7117 · Cited by 702 · see citing works
Complete genomic and epigenetic maps of human centromeres
Altemose, N., Logsdon, G. A., Bzikadze, A. V., Sidhwani, P., Langley, S. A., Caldas, G. V., Hoyt, S. J., Uralsky, L., Ryabov, F. D., Shew, C. J., et al. (2022) · Science · doi:10.1126/science.abl4178 · Cited by 618 · see citing works
The Human Pangenome Project: a global resource to map genomic diversity
Wang, T., Antonacci-Fulton, L., Howe, K., Lawson, H. A., Lucas, J. K., Phillippy, A. M., Popejoy, A. B., Asri, M., Carson, C., Chaisson, M. J. P., et al. (2022) · Nature · doi:10.1038/s41586-022-04601-8 · Cited by 494 · see citing works
Self-citationA complete reference genome improves analysis of human genetic variation
Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., et al. (2022) · Science · doi:10.1126/science.abl3533 · Cited by 441 · see citing works
Ancient gene linkages support ctenophores as sister to other animals
Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature · doi:10.1038/s41586-023-05936-6 · Cited by 362 · see citing works
Towards population-scale long-read sequencing
De Coster, W., Weissensteiner, M. H., & Sedlazeck, F. J. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00367-3 · Cited by 323 · see citing works
Segmental duplications and their variation in a complete human genome
Vollger, M. R., Guitart, X., Dishuck, P. C., Mercuri, L., Harvey, W. T., Gershman, A., Diekhans, M., Sulovari, A., Munson, K. M., Lewis, A. P., et al. (2022) · Science · doi:10.1126/science.abj6965 · Cited by 350 · see citing works
Ebler, J., Ebert, P., Clarke, W. E., Rausch, T., Audano, P. A., Houwaart, T., Mao, Y., Korbel, J. O., Eichler, E. E., Zody, M. C., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01043-w · Cited by 277 · see citing works
Curated variation benchmarks for challenging medically relevant autosomal genes
Wagner, J., Olson, N. D., Harris, L., McDaniel, J., Cheng, H., Fungtammasan, A., Hwang, Y.-C., Gupta, R., Wenger, A. M., Rowell, W. J., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01158-1 · Cited by 241 · see citing works
Self-citationSemi-automated assembly of high-quality diploid human reference genomes
Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., et al. (2022) · Nature · doi:10.1038/s41586-022-05325-5 · Cited by 209 · see citing works
Self-citationLong-Read DNA Sequencing: Recent Advances and Remaining Challenges
Warburton, P. E., & Sebra, R. P. (2023) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-101722-103045 · Cited by 163 · see citing works
Increased mutation and gene conversion within human segmental duplications
Vollger, M. R., Dishuck, P. C., Harvey, W. T., DeWitt, W. S., Guitart, X., Goldberg, M. E., Rozanski, A. N., Lucas, J., Asri, M., Human Pangenome Reference Consortium, et al. (2023) · Nature · doi:10.1038/s41586-023-05895-y · Cited by 104 · see citing works
Self-citationZhou, Y., Yang, L., Han, X., Han, J., Hu, Y., Li, F., Xia, H., Peng, L., Boschiero, C., Rosen, B. D., et al. (2022) · Genome Research · doi:10.1101/gr.276550.122 · Cited by 89 · see citing works
Analysis and benchmarking of small and large genomic variants across tandem repeats
English, A. C., Dolzhenko, E., Ziaei Jam, H., McKenzie, S. K., Olson, N. D., De Coster, W., Park, J., Gu, B., Wagner, J., Eberle, M. A., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02225-z · Cited by 68 · see citing works
Gaps and complex structurally variant loci in phased genome assemblies
Porubsky, D., Vollger, M. R., Harvey, W. T., Rozanski, A. N., Ebert, P., Hickey, G., Hasenfeld, P., Sanders, A. D., Stober, C., Human Pangenome Reference Consortium, et al. (2023) · Genome Research · doi:10.1101/gr.277334.122 · Cited by 58 · see citing works
The complete telomere-to-telomere sequence of a mouse genome
Liu, J., Li, Q., Hu, Y., Yu, Y., Zheng, K., Li, D., Qin, L., & Yu, X. (2024) · Science · doi:10.1126/science.adq8191 · Cited by 57 · see citing works
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 · see citing works
The vast majority of somatic mutations in plants are layer-specific
Goel, M., Campoy, J. A., Krause, K., Baus, L. C., Sahu, A., Sun, H., Walkemeier, B., Marek, M., Beaudry, R., Ruiz, D., et al. (2024) · Genome Biology · doi:10.1186/s13059-024-03337-0 · Cited by 31 · see citing works
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) · Genome Biology · doi:10.1186/s13059-023-02863-7 · Cited by 28 · see citing works
Nhu, N. T. K., Phan, M.-D., Hancock, S. J., Peters, K. M., Alvarez-Fraga, L., Forde, B. M., Andersen, S. B., Miliya, T., Harris, P. N., Beatson, S. A., et al. (2024) · eLife · doi:10.7554/elife.91853.3 · Cited by 41 · see citing works
Milia, S., Leonard, A. S., Mapel, X. M., Bernal Ulloa, S. M., Drögemüller, C., & Pausch, H. (2025) · Genome Research · doi:10.1101/gr.279064.124 · Cited by 22 · see citing works
Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle
Xia, X., Wang, F., Luo, X., Li, S., Lyu, Y., Zheng, Y., Ma, Z., Qu, K., Song, R., Liu, J., et al. (2025) · Advanced Science · doi:10.1002/advs.202503258 · Cited by 14 · see citing works
Liu, G. E. (2025) · Journal of Animal Science and Biotechnology · doi:10.1186/s40104-025-01294-7 · Cited by 8 · see citing works
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., Concepcion, G. T., Feng, X., Zhang, H., & Li, H.
- Affiliations
- Harvard University (US)
- Pacific Biosciences (United States) (US)
- Georgia Institute of Technology (US)
- Corresponding author
- Li, Heng
- Venue
- Nature Methods
- Published
- 2021-02
- Volume
- 18
- Issue
- 2
- Pages
- 170-175
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC7961889
- OpenAlex
- W3047598142
- Cited by
- 5,859
- References
- 40
- Citations by year
- 2026: 1431 · 2025: 1650 · 2024: 1401 · 2023: 850 · 2022: 381 · 2021: 140 · 2020: 3 · 2019: 1
- FWCI
- 226.27
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University) (cc-by)
- Funders
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (R01HG010040, U01HG010971, U41HG010972)
- 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 › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- haplotype-resolved genome assembly, de novo genome assembly, Hifiasm, trio binning, heterozygous alleles, long-read sequencing, hexaploid genome, Sequoia sempervirens
- MeSH terms
- Algorithms, Haplotypes, Genome, Sequence Analysis, DNA
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
