Succinct colored de Bruijn graphs | Zendy

Martin D. Muggli | Zendy; Alexander Bowe | Zendy; Noelle Noyes | Zendy; Paul S. Morley | Zendy; K. E. Belk | Zendy; Robert A. Raymond | Zendy; Travis Gagie | Zendy; Simon J. Puglisi | Zendy; Christina Boucher | Zendy

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Succinct colored de Bruijn graphs

Author(s) -

Martin D. Muggli,

Alexander Bowe,

Noelle Noyes,

Paul S. Morley,

K. E. Belk,

Robert A. Raymond,

Travis Gagie,

Simon J. Puglisi,

Christina Boucher

Publication year - 2017

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btx067

Subject(s) - de bruijn sequence , colored , computer science , de bruijn graph , combinatorics , mathematics , sociology , anthropology

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.

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