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Haplotype-resolved assembly of diploid genomes without parental data

Nature Biotechnology volume 40, pages 1332–1335 (2022)Cite this article

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Abstract

Routine haplotype-resolved genome assembly from single samples remains an unresolved problem. Here we describe an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of similar quality to the best pedigree-based assemblies.

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Fig. 1: Haplotype-resolved assembly using Hi-C data.

Data availability

Human reference genome: GRCh38; CHM13 genome: GCA_009914755.3; HG002 HiFi reads: SRR10382244, SRR10382245, SRR10382248 and SRR10382249; HG002 Hi-C reads: ‘HG002.HiC_1*.fastq.gz’ from https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0; HG002 parental short reads: from the same HG002 data freeze; HG00733 HiFi reads: ERX3831682; HG00733 Hi-C reads: SRR11347815; HG00733 parental short reads: ERR3241754 for HG00731 (father) and ERR3241755 for HG00732 (mother); European badger: PRJEB46293; sterlet: PRJEB19273; South Island takahe: https://vgp.github.io/genomeark/Porphyrio_hochstetteri/; and black rhinoceros: https://vgp.github.io/genomeark/Diceros_bicornis/. All evaluated assemblies are available at https://zenodo.org/record/5948487 and https://zenodo.org/record/5953248.

Code availability

Hifiasm is available at https://github.com/chhylp123/hifiasm.

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Acknowledgements

This study was supported by the US National Institutes of Health (grants R01HG010040, U01HG010961, U01HG010971 and U41HG010972 to H.L.) and Howard Hughes Medical Institute funds to E.D.J. We thank members of the Vertebrate Genome Lab at The Rockefeller University and the Sanger genome team at the Sanger Institute for help with producing data for the non-human vertebrate species. Presentation and analyses of the completed reference genome assemblies will be reported on separately. We also thank the Human Pangenome Reference Consortium for making the HiFi and Hi-C data of HG002 and HG00733 publicly available. K.-P.K. thanks the International Rhino Foundation for providing funding to generate the black rhinoceros assembly (grant no. R-2018-1). The South Island takahe genome was funded by Revive and Restore and the University of Otago. The South Island takahe reference genome was created in direct collaboration with the Takahē Recovery Team (Department of Conservation, New Zealand) and Ngāi Tahu, the Māori kaitiaki (‘guardians’) of this taonga (‘treasured’) species. Sequencing of the takahe genome was funded by Revive and Restore and the University of Otago. L.U. was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation, the Revive and Restore Catalyst Science Fund and the University of Otago.

Author information

Authors and Affiliations

  1. Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA

    Haoyu Cheng & Heng Li

  2. Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA

    Haoyu Cheng & Heng Li

  3. The Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA

    Erich D. Jarvis & Olivier Fedrigo

  4. Howard Hughes Medical Institute, Chevy Chase, MD, USA

    Erich D. Jarvis

  5. Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA

    Klaus-Peter Koepfli

  6. Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington D.C., USA

    Klaus-Peter Koepfli

  7. ITMO University, Computer Technologies Laboratory, St. Petersburg, Russia

    Klaus-Peter Koepfli

  8. Department of Anatomy, University of Otago, Dunedin, New Zealand

    Lara Urban & Neil J. Gemmell

Authors
  1. Haoyu Cheng
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  2. Erich D. Jarvis
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  3. Olivier Fedrigo
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  4. Klaus-Peter Koepfli
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  5. Lara Urban
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  7. Heng Li
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Contributions

H.C. and H.L. designed the algorithm, implemented hifiasm and drafted the manuscript. H.C. benchmarked hifiasm and other assemblers. E.D.J. and O.F. coordinated generation of the non-human vertebrate species data as part of the vertebrate genomes project. K.-P.K. sponsored the black rhinoceros genome. L.U. obtained the South Island takahe samples, all necessary permits and funding for the South Island takahe reference genome. L.U. and N.G. sponsored the South Island takahe genome.

Corresponding author

Correspondence to Heng Li.

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Competing interests

H.L. is a consultant of Integrated DNA Technologies and is on the Scientific Advisory Boards of Sentieon and Innozeen. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Biotechnology thanks Rayan Chikhi, David Rank, Riccardo Vicedomini and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Chromosome-level phasing results for hifiasm (Hi-C) human assemblies.

All contigs were aligned to the T2T CHM13 reference and the Y chromosome of GRCh38, and then the corresponding regions of contigs on the reference were determined based on the alignment results. For each chromosome, the top track and the bottom track indicate haplotype 1 contigs and haplotype 2 contigs, respectively. The phase density of contigs was calculated by the parental short reads. Gray bars indicate centromeric regions. (a) Chromosome-level phasing results for HG002 with 30X HiFi and 30X Hi-C. (b) Chromosome-level phasing results for HG00733 with 30X HiFi and 30X Hi-C.

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Supplementary Information

Supplementary Section 1, Tables 1–3 and Fig. 1.

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Cheng, H., Jarvis, E.D., Fedrigo, O. et al. Haplotype-resolved assembly of diploid genomes without parental data. Nat Biotechnol 40, 1332–1335 (2022). https://doi.org/10.1038/s41587-022-01261-x

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