Succinct colored de Bruijn graphs

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Abstract

Motivation

In 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.

Results

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.

Availability and Implementation

https://github.com/cosmo-team/cosmo/tree/VARI

Contact

martin.muggli@colostate.edu

Supplementary information

Supplementary data are available at Bioinformatics online.

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