Finished bacterial genomes from shotgun sequence data

  1. David B. Jaffe3
  1. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    1. 1 These authors contributed equally to this work.

    • 2 Present address: New York Genome Center, 590 Madison Avenue, New York, NY 10022, USA.

    Abstract

    Exceptionally accurate genome reference sequences have proven to be of great value to microbial researchers. Thus, to date, about 1800 bacterial genome assemblies have been “finished” at great expense with the aid of manual laboratory and computational processes that typically iterate over a period of months or even years. By applying a new laboratory design and new assembly algorithm to 16 samples, we demonstrate that assemblies exceeding finished quality can be obtained from whole-genome shotgun data and automated computation. Cost and time requirements are thus dramatically reduced.

    Footnotes

    • 3 Corresponding author

      E-mail jaffe{at}broadinstitute.org

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.141515.112.

      Freely available online through the Genome Research Open Access option.

    • Received April 9, 2012.
    • Accepted June 13, 2012.

    This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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