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

Oxford Nanopore Sequencing and de novo Assembly of a Eukaryotic Genome

Sara Goodwin, James Gurtowski, Scott Ethe-Sayers, Panchajanya Deshpande, Michael C. Schatz, W. Richard McCombie
doi: https://doi.org/10.1101/013490
Sara Goodwin
Cold Spring Harbor Laboratory, 1 Bungtown Rd. Cold Spring Harbor, NY 11724
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
James Gurtowski
Cold Spring Harbor Laboratory, 1 Bungtown Rd. Cold Spring Harbor, NY 11724
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Scott Ethe-Sayers
Cold Spring Harbor Laboratory, 1 Bungtown Rd. Cold Spring Harbor, NY 11724
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Panchajanya Deshpande
Cold Spring Harbor Laboratory, 1 Bungtown Rd. Cold Spring Harbor, NY 11724
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael C. Schatz
Cold Spring Harbor Laboratory, 1 Bungtown Rd. Cold Spring Harbor, NY 11724
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
W. Richard McCombie
Cold Spring Harbor Laboratory, 1 Bungtown Rd. Cold Spring Harbor, NY 11724
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Monitoring the progress of DNA through a pore has been postulated as a method for sequencing DNA for several decades1,2. Recently, a nanopore instrument, the Oxford Nanopore MinION, has become available3. Here we describe our sequencing of the S. cerevisiae genome. We describe software developed to make use of these data as existing packages were incapable of assembling long reads at such high error rate (∼35% error). With these methods we were able to error correct and assemble the nanopore reads de novo, producing an assembly that is contiguous and accurate: with a contig N50 length of 479kb, and has greater than 99% consensus identity when compared to the reference. The assembly with the long nanopore reads was able to correctly assemble gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in an assembly using Illumina sequencing alone (with a contig N50 of only 59,927bp).

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 4.0 International license.
Back to top
PreviousNext
Posted January 06, 2015.
Download PDF

Supplementary Material

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.
Oxford Nanopore Sequencing and de novo Assembly of a Eukaryotic Genome
(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
Oxford Nanopore Sequencing and de novo Assembly of a Eukaryotic Genome
Sara Goodwin, James Gurtowski, Scott Ethe-Sayers, Panchajanya Deshpande, Michael C. Schatz, W. Richard McCombie
bioRxiv 013490; doi: https://doi.org/10.1101/013490
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Oxford Nanopore Sequencing and de novo Assembly of a Eukaryotic Genome
Sara Goodwin, James Gurtowski, Scott Ethe-Sayers, Panchajanya Deshpande, Michael C. Schatz, W. Richard McCombie
bioRxiv 013490; doi: https://doi.org/10.1101/013490

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

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3686)
  • Biochemistry (7774)
  • Bioengineering (5668)
  • Bioinformatics (21245)
  • Biophysics (10563)
  • Cancer Biology (8162)
  • Cell Biology (11915)
  • Clinical Trials (138)
  • Developmental Biology (6738)
  • Ecology (10388)
  • Epidemiology (2065)
  • Evolutionary Biology (13843)
  • Genetics (9694)
  • Genomics (13056)
  • Immunology (8123)
  • Microbiology (19956)
  • Molecular Biology (7833)
  • Neuroscience (42973)
  • Paleontology (318)
  • Pathology (1276)
  • Pharmacology and Toxicology (2256)
  • Physiology (3350)
  • Plant Biology (7208)
  • Scientific Communication and Education (1309)
  • Synthetic Biology (1999)
  • Systems Biology (5528)
  • Zoology (1126)