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Genome assembly in the telomere-to-telomere era

Nature Reviews Genetics (2024)Cite this article

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Abstract

Genome sequences largely determine the biology and encode the history of an organism, and de novo assembly — the process of reconstructing the genome sequence of an organism from sequencing reads — has been a central problem in bioinformatics for four decades. Until recently, genomes were typically assembled into fragments of a few megabases at best, but now technological advances in long-read sequencing enable the near-complete assembly of each chromosome — also known as telomere-to-telomere assembly — for many organisms. Here, we review recent progress on assembly algorithms and protocols, with a focus on how to derive near-telomere-to-telomere assemblies. We also discuss the additional developments that will be required to resolve remaining assembly gaps and to assemble non-diploid genomes.

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Fig. 1: Strategy for near-telomere-to-telomere assembly.
Fig. 2: Types of phased assembly of diploid samples.
Fig. 3: Assembly with overlap graphs.
Fig. 4: De Bruijn graphs.

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Acknowledgements

We are grateful to H. Cheng and C. Zhou for their helpful comments on the manuscript.

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

    Heng Li

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

    Heng Li

  3. Department of Genetics, Cambridge University, Cambridge, UK

    Richard Durbin

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Li, H., Durbin, R. Genome assembly in the telomere-to-telomere era. Nat Rev Genet (2024). https://doi.org/10.1038/s41576-024-00718-w

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