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Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing

Konstantin Berlin, Sergey Koren, Chen-Shan Chin, James Drake, Jane M. Landolin, Adam M. Phillippy
doi: https://doi.org/10.1101/008003
Konstantin Berlin
1Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
2Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
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Sergey Koren
3National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA
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  • For correspondence: korens@nbacc.net
Chen-Shan Chin
4Pacific Biosciences, Menlo Park, CA 94025, USA
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James Drake
4Pacific Biosciences, Menlo Park, CA 94025, USA
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Jane M. Landolin
4Pacific Biosciences, Menlo Park, CA 94025, USA
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Adam M. Phillippy
3National Biodefense Analysis and Countermeasures Center, Frederick, MD 21702, USA
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ABSTRACT

We report reference-grade de novo assemblies of four model organisms and the human genome from single-molecule, real-time (SMRT) sequencing. Long-read SMRT sequencing is routinely used to finish microbial genomes, but the available assembly methods have not scaled well to larger genomes. Here we introduce the MinHash Alignment Process (MHAP) for efficient overlapping of noisy, long reads using probabilistic, locality-sensitive hashing. Together with Celera Assembler, MHAP was used to reconstruct the genomes of Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, and human from high-coverage SMRT sequencing. The resulting assemblies include fully resolved chromosome arms and close persistent gaps in these important reference genomes, including heterochromatic and telomeric transition sequences. For D. melanogaster, MHAP achieved a 600-fold speedup relative to prior methods and a cloud computing cost of a few hundred dollars. These results demonstrate that single-molecule sequencing alone can produce near-complete eukaryotic genomes at modest cost.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 14, 2014.
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Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing
Konstantin Berlin, Sergey Koren, Chen-Shan Chin, James Drake, Jane M. Landolin, Adam M. Phillippy
bioRxiv 008003; doi: https://doi.org/10.1101/008003
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Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing
Konstantin Berlin, Sergey Koren, Chen-Shan Chin, James Drake, Jane M. Landolin, Adam M. Phillippy
bioRxiv 008003; doi: https://doi.org/10.1101/008003

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