International Workshop on Algorithms in Bioinformatics

WABI 2015: Algorithms in Bioinformatics pp 175-188

Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches

  • Giles Miclotte
  • Mahdi Heydari
  • Piet Demeester
  • Pieter Audenaert
  • Jan Fostier
Conference paper

DOI: 10.1007/978-3-662-48221-6_13

Part of the Lecture Notes in Computer Science book series (LNCS, volume 9289)
Cite this paper as:
Miclotte G., Heydari M., Demeester P., Audenaert P., Fostier J. (2015) Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches. In: Pop M., Touzet H. (eds) Algorithms in Bioinformatics. WABI 2015. Lecture Notes in Computer Science, vol 9289. Springer, Berlin, Heidelberg

Abstract

Third generation sequencing platforms produce longer reads with higher error rates than second generation sequencing technologies. While the improved read length can provide useful information for downstream analysis, underlying algorithms are challenged by the high error rate. Error correction methods in which accurate short reads are used to correct noisy long reads appear to be attractive to generate high-quality long reads. Methods that align short reads to long reads do not optimally use the information contained in the second generation data, and suffer from large runtimes. Recently, a new hybrid error correcting method has been proposed, where the second generation data is first assembled into a de Bruijn graph, on which the long reads are then aligned. In this context we present Jabba, a hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to our method is that this mapping is constructed with a seed and extend methodology, using maximal exact matches as seeds. In addition to benchmark results, certain theoretical results concerning the possibilities and limitations of the use of maximal exact matches in the context of third generation reads are presented.

Keywords

Sequence analysis Error correction de Bruijn graph Maximal exact matches 

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Giles Miclotte
    • 1
  • Mahdi Heydari
    • 1
  • Piet Demeester
    • 1
  • Pieter Audenaert
    • 1
  • Jan Fostier
    • 1
  1. 1.Department of Information Technology, Internet Based Communication Networks and Services (IBCN)Ghent University - IMindsGentBelgium

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