Succinct Colored de Bruijn Graphs

Keith Belk; Christina Boucher; Alexander Bowe; Travis Gagie; Paul Morley; Martin D Muggli; Noelle R Noyes; Simon J Puglisi; Rober Raymond

doi:10.1101/040071

bioRxiv · 10.1101/040071

Succinct Colored de Bruijn Graphs

Keith Belk·Christina Boucher·Alexander Bowe·Travis Gagie·Paul Morley·Martin D Muggli·Noelle R Noyes·Simon J Puglisi·Rober Raymond

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Abstract

Iqbal et al. (Nature Genetics, 2012) 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 require additional information to be succinctly encoded as well as support for non-standard traversal operations. Our 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.

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Keith Belk, Christina Boucher, Alexander Bowe, Travis Gagie, Paul Morley, Martin D Muggli, Noelle R Noyes, Simon J Puglisi, Rober Raymond. 2016-02-18. Succinct Colored de Bruijn Graphs. https://doi.org/10.1101/040071

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