Scaffolding and validation of bacterial genome assemblies using optical restriction maps

Bioinformatics. 2008 May 15;24(10):1229-35. doi: 10.1093/bioinformatics/btn102. Epub 2008 Mar 20.


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

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Validation Study

MeSH terms

  • Algorithms*
  • Base Sequence
  • Chromosome Mapping / methods*
  • Genome, Bacterial / genetics*
  • Molecular Sequence Data
  • Optics and Photonics*
  • Restriction Mapping / methods*
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*