We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Scaffolding and validation of bacterial genome assemblies using optical restriction maps.
- Authors
Niranjan Nagarajan; Timothy D. Read; Mihai Pop
- 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@umiacs.umd.edu
- Publication
Bioinformatics, 2008, Vol 24, Issue 10, p1229
- ISSN
1367-4803
- Publication type
Academic Journal
- DOI
10.1093/bioinformatics/btn102