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BAIT: Organizing genomes and mapping rearrangements in single cells

Mark Hills1*, Kieran O’Neill1, Ester Falconer1, Ryan Brinkman1 and Peter M Lansdorp123*

Author Affiliations

1 Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada

2 Division of Hematology, Department of Medicine, University of British Columbia, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada

3 European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, NL-9713 AV Groningen, The Netherlands

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Genome Medicine 2013, 5:82  doi:10.1186/gm486

Published: 13 September 2013

Abstract

Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, identifying approximately 21 Mb of incorrectly oriented fragments and placing over half (2.6 Mb) of the orphan fragments in mm10/GRCm38. BAIT also stratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. BAIT is available at http://sourceforge.net/projects/bait/ webcite.