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Bioinformatics Advance Access originally published online on December 5, 2007
Bioinformatics 2008 24(1):42-45; doi:10.1093/bioinformatics/btm542
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© 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, 2Agencourt Bioscience Inc., Beverly, MA and 3The J. Craig Venter Instutute, Rockville, MD, USA

*To whom correspondence should be addressed.


  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: alekseyz{at}ipst.umd.edu

Associate Editor: Alex Bateman

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

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