Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads

  • Claire Lemaitre
  • Liviu Ciortuz
  • Pierre Peterlongo
Conference paper

DOI: 10.1007/978-3-319-07953-0_10

Part of the Lecture Notes in Computer Science book series (LNCS, volume 8542)
Cite this paper as:
Lemaitre C., Ciortuz L., Peterlongo P. (2014) Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Reads. In: Dediu AH., Martín-Vide C., Truthe B. (eds) Algorithms for Computational Biology. AlCoB 2014. Lecture Notes in Computer Science, vol 8542. Springer, Cham

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 positives 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. Applied 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.

Keywords

structural variant NGS reference-free de Bruijn graph 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Claire Lemaitre
    • 1
  • Liviu Ciortuz
    • 1
    • 2
  • Pierre Peterlongo
    • 1
  1. 1.INRIA/IRISA/GenScaleRennes cedexFrance
  2. 2.Faculty of Computer Science IasiRomania

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