Skip Navigation



Bioinformatics Advance Access published online on December 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm542
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrowOA All Versions of this Article:
24/1/42    most recent
btm542v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Google Scholar
Right arrow Articles by Zimin, A. V
Right arrow Articles by Yorke, J. A.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Zimin, A. V
Right arrow Articles by Yorke, J. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Assembly Reconciliation

Aleksey V Zimin *,1, Douglas R. Smith 2, Granger Sutton 3 and James A. Yorke 1

1IPST, University of Maryland, College Park, 2USA; Agencourt Bioscience Inc., Beverly, MA., USA; 3The J. Craig Venter Instutute, Rockville, MD, USA.

*To whom correspondence should be addressed. Dr. Aleksey V Zimin, E-mail: alekseyz{at}ipst.umd.edu


  Abstract

Motivation: Many genomes are sequenced by a collaboration of several centers, and then each center produces an assembly using their own assembly software. The collaborators then pick the draft assembly that they judge to be the best and the information contained in the other assemblies is usually not used.

Methods: We have developed a technique that we call assembly reconciliation that can merge draft genome assemblies. It takes one draft assembly, detects apparent errors, and, when possible, patches the problem areas using pieces from alternative draft assemblies. It also closes gaps in places where one of the alternative assemblies has spanned the gap correctly.

Results: Using the Assembly Reconciliation technique we produced reconciled assemblies of six Drosophila species in collaboration with Agencourt Bioscience and The J. Craig Venter Institute. These assemblies are now the official (CAF1) assemblies used for analysis. We also produced a reconciled assembly of Rhesus Macaque genome, and this assembly is available from our website http://www.genome.umd.edu.

Availability: The reconciliation software is available for download from http://www.genome.umd.edu/software.htm.

Contact: Aleksey Zimin alekseyz{at}ipst.umd.edu.

Associate Editor: Dr. Alex Bateman

Received on August 7, 2007; revised on October 15, 2007; accepted on October 22, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.