Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads

Claire Lemaitre 1, * Liviu Ciortuz 2 Pierre Peterlongo 1
* Corresponding author
1 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : We propose a formal model and an algorithm for detecting inversion breakpoints without a reference genome, directly from raw NGS data. This model is characterized by a fixed size topological pattern in the de Bruijn Graph. We describe precisely the possible sources of false pos- itives and false negatives and we additionally propose a sequence-based filter giving a good trade-off between precision and recall of the method. We implemented these ideas in a prototype called TakeABreak. Ap- plied on simulated inversions in genomes of various complexity (from E. coli to a human chromosome dataset), TakeABreak provided promising results with a low memory footprint and a small computational time.
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Claire Lemaitre, Liviu Ciortuz, Pierre Peterlongo. Mapping-free and assembly-free discovery of inversion breakpoints from raw NGS reads. Algorithms for Computational Biology, Jul 2014, Tarragona, Spain. pp.119-130, ⟨10.1007/978-3-319-07953-0_10⟩. ⟨hal-01063157v3⟩

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