IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v8y2017i1d10.1038_ncomms14515.html
   My bibliography  Save this article

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

Author

Listed:
  • Minh Duc Cao

    (Institute for Molecular Bioscience, University of Queensland)

  • Son Hoang Nguyen

    (Institute for Molecular Bioscience, University of Queensland)

  • Devika Ganesamoorthy

    (Institute for Molecular Bioscience, University of Queensland)

  • Alysha G. Elliott

    (Institute for Molecular Bioscience, University of Queensland)

  • Matthew A. Cooper

    (Institute for Molecular Bioscience, University of Queensland)

  • Lachlan J. M. Coin

    (Institute for Molecular Bioscience, University of Queensland)

Abstract

Third generation sequencing technologies provide the opportunity to improve genome assemblies by generating long reads spanning most repeat sequences. However, current analysis methods require substantial amounts of sequence data and computational resources to overcome the high error rates. Furthermore, they can only perform analysis after sequencing has completed, resulting in either over-sequencing, or in a low quality assembly due to under-sequencing. Here we present npScarf, which can scaffold and complete short read assemblies while the long read sequencing run is in progress. It reports assembly metrics in real-time so the sequencing run can be terminated once an assembly of sufficient quality is obtained. In assembling four bacterial and one eukaryotic genomes, we show that npScarf can construct more complete and accurate assemblies while requiring less sequencing data and computational resources than existing methods. Our approach offers a time- and resource-effective strategy for completing short read assemblies.

Suggested Citation

  • Minh Duc Cao & Son Hoang Nguyen & Devika Ganesamoorthy & Alysha G. Elliott & Matthew A. Cooper & Lachlan J. M. Coin, 2017. "Scaffolding and completing genome assemblies in real-time with nanopore sequencing," Nature Communications, Nature, vol. 8(1), pages 1-10, April.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14515
    DOI: 10.1038/ncomms14515
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms14515
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms14515?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Son Hoang Nguyen & Minh Duc Cao & Lachlan J M Coin, 2021. "Real-time resolution of short-read assembly graph using ONT long reads," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-18, January.
    2. Mohamed Awad & Xiangchao Gan, 2023. "GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14515. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.