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Bioinformatics Advance Access originally published online on March 20, 2008
Bioinformatics 2008 24(10):1229-1235; doi:10.1093/bioinformatics/btn102
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© 2008 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.

Scaffolding and validation of bacterial genome assemblies using optical restriction maps

Niranjan Nagarajan 1, Timothy D. Read 2 and Mihai Pop 1,*

1University of Maryland, College Park, MD 20742 and 2Biological Defense Research Directorate, Naval Medical Research Center and Henry M. Jackson Foundation, 12300 Washington Ave, Rockville, MD 20852, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing technologies, such as the short length of the sequencing reads and absence of mate-pair information. In this article we propose methods to overcome such limitations by incorporating information from optical restriction maps.

Results: We demonstrate the robustness of our methods to sequencing and assembly errors using extensive experiments on simulated datasets. We then present the results obtained by applying our algorithms to data generated from two bacterial genomes Yersinia aldovae and Yersinia kristensenii. The resulting assemblies contain a single scaffold covering a large fraction of the respective genomes, suggesting that the careful use of optical maps can provide a cost-effective framework for the assembly of genomes.

Availability: The tools described here are available as an open-source package at ftp://ftp.cbcb.umd.edu/pub/software/soma

Contact: mpop{at}umiacs.umd.edu

Associate Editor: Alfonso Valencia

Received on December 18, 2007; revised on March 5, 2008; accepted on March 16, 2008

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