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Bioinformatics Vol. 18 no. 11 2002
Pages 1418-1426
© 2002 Oxford University Press

Identification of mixups among DNA sequencing plates

Nikola Stojanovic 1,*, Jean L. Chang 1, Jessica Lehoczky 1,2, Michael C. Zody 1 and Ken Dewar 1

1 Whitehead Institute, Center for Genome Research, 320 Charles Street, Cambridge MA 02141, UK
2 Department of Human Genetics, University of Michigan, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
3 Montreal Genome Centre, The Research Institute of the McGill University Health Centre, 1650 Cedar Avenue, Montreal, Quebec, Canada H3G 1A4

Received on January 10, 2002 ; revised on April 13, 2002 ; accepted on May 9, 2002

Motivation: During the process of high-throughput genome sequencing there are opportunities for mixups of reagents and data associated with particular projects. The sequencing templates or sequence data generated for an assembly may become contaminated with reagents or sequences from another project, resulting in poorer quality and inaccurate assemblies.

Results: We have developed a system to assess sequence assemblies and monitor for laboratory mixups. We describe several methods for testing the consistency of assemblies and resolving mixed ones. We use statistical tests to evaluate the distribution of sequencing reads from different plates into contigs, and a graph-based approach to resolve situations where data has been inappropriately combined. While these methods have been designed for use in a high-throughput DNA sequencing environment processing thousands of clones, they can be applied in any situation where distinct sequencing projects are performed at redundant coverage.

Availability: Our software is available for downloading from: ftp-genome.wi.mit.edu/distribution/mixups_detection

Contact: nick{at}genome.wi.mit.edu

* To whom correspondence should be addressed.


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