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Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

Nature Biotechnology volume 33, pages 623–630 (2015)Cite this article

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A Corrigendum to this article was published on 08 October 2015

This article has been updated

Abstract

Long-read, single-molecule real-time (SMRT) sequencing is routinely used to finish microbial genomes, but available assembly methods have not scaled well to larger genomes. We introduce the MinHash Alignment Process (MHAP) for overlapping noisy, long reads using probabilistic, locality-sensitive hashing. Integrating MHAP with the Celera Assembler enabled reference-grade de novo assemblies of Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster and a human hydatidiform mole cell line (CHM1) from SMRT sequencing. The resulting assemblies are highly continuous, include fully resolved chromosome arms and close persistent gaps in these reference genomes. Our assembly of D. melanogaster revealed previously unknown heterochromatic and telomeric transition sequences, and we assembled low-complexity sequences from CHM1 that fill gaps in the human GRCh38 reference. Using MHAP and the Celera Assembler, single-molecule sequencing can produce de novo near-complete eukaryotic assemblies that are 99.99% accurate when compared with available reference genomes.

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Figure 1: Rapid overlapping of noisy reads using MinHash sketches.
Figure 2: Simulated MHAP performance for various sketch sizes and read lengths.
Figure 3: Single-contig assembly of D. melanogaster chromosome arm 3L.
Figure 4: Continuity and putative GRCh38 gap closures of the CHM1 assembly.

Change history

  • 06 October 2015

    In the version of this article initially published, equation 9 appeared incorrectly. The equation has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We are indebted to C. Bergman of the University of Manchester for his considered advice throughout this project and editing of an early version of this manuscript. We also thank Pacific Biosciences and all those involved in generating and freely releasing the data analyzed here. The contributions of S.K. and A.M.P. were funded under Agreement No. HSHQDC-07-C-00020 awarded by the Department of Homeland Security Science and Technology Directorate (DHS/S&T) for the management and operation of the National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and Development Center. The views and conclusions contained in this document are those of the authors and should not be interpreted as necessarily representing the official policies, either expressed or implied, of the US Department of Homeland Security. In no event shall the DHS, NBACC or Battelle National Biodefense Institute (BNBI) have any responsibility or liability for any use, misuse, inability to use, or reliance upon the information contained herein. The Department of Homeland Security does not endorse any products or commercial services mentioned in this publication.

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Author notes

  1. Konstantin Berlin and Sergey Koren: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA

    Konstantin Berlin

  2. Institute for Advanced Computer Studies, University of Maryland, College Park, Maryland, USA

    Konstantin Berlin

  3. Invincea Labs, Arlington, Virginia, USA

    Konstantin Berlin

  4. National Biodefense Analysis and Countermeasures Center, Frederick, Maryland, USA

    Sergey Koren & Adam M Phillippy

  5. Pacific Biosciences of California, Inc., Menlo Park, California, USA

    Chen-Shan Chin, James P Drake & Jane M Landolin

Authors
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Contributions

K.B. and S.K. conceived, designed and implemented the MHAP algorithm. C.S.C. and J.P.D. conceived, designed and implemented the consensus algorithms. S.K. ran and analyzed the genome assemblies. J.M.L. coordinated data release and assisted with pipeline executions. C.S.C. and S.K. performed cloud-computing experiments. K.B., S.K. and A.M.P. drafted the manuscript. A.M.P. coordinated the project. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Sergey Koren.

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Berlin, K., Koren, S., Chin, CS. et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 33, 623–630 (2015). https://doi.org/10.1038/nbt.3238

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