1Department of Computer Science, Colorado State University, Fort Collins, CO, USA2Department of Informatics, National Institute of Informatics, Chiyoda-ku, Tokyo, Japan3Department of Clinical Sciences4Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA5School of Computer Science and Telecommunications, Diego Portales University and CEBIB, Santiago, Chile6Department of Computer Science, University of Helsinki, Helsinki, Finland
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MotivationIn 2012, Iqbal et al. introduced the colored de Bruijn graph, a variant of the classic de Bruijn graph, which is aimed at ‘detecting and genotyping simple and complex genetic variants in an individual or population’. Because they are intended to be applied to massive population level data, it is essential that the graphs be represented efficiently. Unfortunately, current succinct de Bruijn graph representations are not directly applicable to the colored de Bruijn graph, which requires additional information to be succinctly encoded as well as support for non-standard traversal operations.ResultsOur data structure dramatically reduces the amount of memory required to store and use the colored de Bruijn graph, with some penalty to runtime, allowing it to be applied in much larger and more ambitious sequence projects than was previously possible.Availability and Implementationhttps://github.com/cosmo-team/cosmo/tree/VARIContactmartin.email@example.comSupplementary informationSupplementary data are available at Bioinformatics online.