Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Extended haplotype phasing of de novo genome assemblies with FALCON-Phase

Zev N. Kronenberg, Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, Stefan Hiendleder, Olivier Fedrigo, Erich D. Jarvis, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Tim P.L. Smith, Richard J. Hall, Shawn T. Sullivan, Sarah B. Kingan
doi: https://doi.org/10.1101/327064
Zev N. Kronenberg
1Phase Genomics, Seattle, WA, USA
2Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: skingan@pacificbiosciences.com zkronenberg@pacificbiosciences.com
Arang Rhie
3Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sergey Koren
3Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gregory T. Concepcion
2Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul Peluso
2Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Katherine M. Munson
4Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Stefan Hiendleder
5Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Olivier Fedrigo
6Vertebrate Genomes Laboratory, Rockefeller University, New York, NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Erich D. Jarvis
7Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
8Howard Hughes Medical Institute, Chevy Chase, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adam M. Phillippy
3Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Evan E. Eichler
4Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
9Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
John L. Williams
5Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tim P.L. Smith
10US Meat Animal Research Center, ARS USDA, Clay Center, NE, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard J. Hall
3Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shawn T. Sullivan
1Phase Genomics, Seattle, WA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sarah B. Kingan
2Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: skingan@pacificbiosciences.com zkronenberg@pacificbiosciences.com
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

ABSTRACT

Haplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. These assemblies can be created in various ways, such as use of tissues that contain single-haplotype (haploid) genomes, or by co-sequencing of parental genomes, but these approaches can be impractical in many situations. We present FALCON-Phase, which integrates long-read sequencing data and ultra-long-range Hi-C chromatin interaction data of a diploid individual to create high-quality, phased diploid genome assemblies. The method was evaluated by application to three datasets, including human, cattle, and zebra finch, for which high-quality, fully haplotype resolved assemblies were available for benchmarking. Phasing algorithm accuracy was affected by heterozygosity of the individual sequenced, with higher accuracy for cattle and zebra finch (>97%) compared to human (82%). In addition, scaffolding with the same Hi-C chromatin contact data resulted in phased chromosome-scale scaffolds.

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-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted April 19, 2019.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Extended haplotype phasing of de novo genome assemblies with FALCON-Phase
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Extended haplotype phasing of de novo genome assemblies with FALCON-Phase
Zev N. Kronenberg, Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, Stefan Hiendleder, Olivier Fedrigo, Erich D. Jarvis, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Tim P.L. Smith, Richard J. Hall, Shawn T. Sullivan, Sarah B. Kingan
bioRxiv 327064; doi: https://doi.org/10.1101/327064
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Extended haplotype phasing of de novo genome assemblies with FALCON-Phase
Zev N. Kronenberg, Arang Rhie, Sergey Koren, Gregory T. Concepcion, Paul Peluso, Katherine M. Munson, Stefan Hiendleder, Olivier Fedrigo, Erich D. Jarvis, Adam M. Phillippy, Evan E. Eichler, John L. Williams, Tim P.L. Smith, Richard J. Hall, Shawn T. Sullivan, Sarah B. Kingan
bioRxiv 327064; doi: https://doi.org/10.1101/327064

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4115)
  • Biochemistry (8818)
  • Bioengineering (6522)
  • Bioinformatics (23466)
  • Biophysics (11792)
  • Cancer Biology (9212)
  • Cell Biology (13326)
  • Clinical Trials (138)
  • Developmental Biology (7439)
  • Ecology (11416)
  • Epidemiology (2066)
  • Evolutionary Biology (15155)
  • Genetics (10439)
  • Genomics (14045)
  • Immunology (9173)
  • Microbiology (22160)
  • Molecular Biology (8814)
  • Neuroscience (47582)
  • Paleontology (350)
  • Pathology (1429)
  • Pharmacology and Toxicology (2492)
  • Physiology (3731)
  • Plant Biology (8082)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2221)
  • Systems Biology (6039)
  • Zoology (1253)