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HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

View ORCID ProfileSergey Nurk, View ORCID ProfileBrian P. Walenz, View ORCID ProfileArang Rhie, View ORCID ProfileMitchell R. Vollger, View ORCID ProfileGlennis A. Logsdon, Robert Grothe, View ORCID ProfileKaren H. Miga, View ORCID ProfileEvan E. Eichler, View ORCID ProfileAdam M. Phillippy, View ORCID ProfileSergey Koren
doi: https://doi.org/10.1101/2020.03.14.992248
Sergey Nurk
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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Brian P. Walenz
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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Arang Rhie
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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Mitchell R. Vollger
2Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
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Glennis A. Logsdon
2Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
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Robert Grothe
3Pacific Biosciences, Menlo Park, CA USA
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Karen H. Miga
4UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA USA
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Evan E. Eichler
2Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
5Howard Hughes Medical Institute, University of Washington, Seattle, WA USA
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Adam M. Phillippy
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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  • For correspondence: adam.phillippy@nih.gov sergey.koren@nih.gov
Sergey Koren
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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  • For correspondence: adam.phillippy@nih.gov sergey.koren@nih.gov
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Abstract

Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced PacBio HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultra-long Oxford Nanopore reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of 9 complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance towards the complete assembly of human genomes.

Availability HiCanu is implemented within the Canu assembly framework and is available from https://github.com/marbl/canu.

Copyright 
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 4.0 International license.
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Posted March 17, 2020.
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HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Sergey Nurk, Brian P. Walenz, Arang Rhie, Mitchell R. Vollger, Glennis A. Logsdon, Robert Grothe, Karen H. Miga, Evan E. Eichler, Adam M. Phillippy, Sergey Koren
bioRxiv 2020.03.14.992248; doi: https://doi.org/10.1101/2020.03.14.992248
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HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Sergey Nurk, Brian P. Walenz, Arang Rhie, Mitchell R. Vollger, Glennis A. Logsdon, Robert Grothe, Karen H. Miga, Evan E. Eichler, Adam M. Phillippy, Sergey Koren
bioRxiv 2020.03.14.992248; doi: https://doi.org/10.1101/2020.03.14.992248

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