DExTaR: Detection of Exact Tandem Repeats based on the de Bruijn graph

Abstract : Genomes present various types of repeated structures having important roles in the mechanism of evolution. In particular, tandem repeats are analysed for their impact on genetic backgrounds of inherited diseases. However, the main objective of today's de novo assemblers is to output long, high-quality, assembled sequences; to this end, they use heuristic-based assembling procedures, which can leave many repeated regions unassembled - and in particular exact tandem repeats - due to the genomes complexity. In this paper, we propose an effective method, called DExTaR, that improves the detection of exact tandem repeats (ETRs) in any de novo de Bruijn assembly. DExTaR is based on a de Bruijn graph constructed by an assembler and retrieves ETRs left unassembled. When used with the well-known assembler ABySS, we show that DExTaR is able to obtain high quality results in terms of number and length of the detected ETRs.
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Submitted on : Wednesday, February 18, 2015 - 11:44:29 AM
Last modification on : Thursday, April 5, 2018 - 10:36:49 AM

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Guillaume Fertin, Géraldine Jean, Andreea Radulescu, Irena Rusu. DExTaR: Detection of Exact Tandem Repeats based on the de Bruijn graph. IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), Nov 2014, Belfast, Ireland. pp.90-93, ⟨10.1109/BIBM.2014.6999134⟩. ⟨hal-01117967⟩

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