Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph

Haoyu Cheng; Mobin Asri; Julian Lucas; Sergey Koren; Heng Li

doi:10.1038/s41592-024-02269-8

Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph

Nat Methods. 2024 May 10. doi: 10.1038/s41592-024-02269-8. Online ahead of print.

Authors

Haoyu Cheng^{1

2}, Mobin Asri³, Julian Lucas³, Sergey Koren⁴, Heng Li^{5

6}

Affiliations

¹ Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
² Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
³ Genomics Institute, University of California, Santa Cruz, CA, USA.
⁴ Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
⁵ Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA. hli@ds.dfci.harvard.edu.
⁶ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. hli@ds.dfci.harvard.edu.

PMID: 38730258
DOI: 10.1038/s41592-024-02269-8

Abstract

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.

Abstract

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