Annual International Conference on Research in Computational Molecular Biology

RECOMB 2010: Research in Computational Molecular Biology pp 384-396

Seed Design Framework for Mapping SOLiD Reads

  • Laurent Noé
  • Marta Gîrdea
  • Gregory Kucherov
Conference paper

DOI: 10.1007/978-3-642-12683-3_25

Volume 6044 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Noé L., Gîrdea M., Kucherov G. (2010) Seed Design Framework for Mapping SOLiD Reads. In: Berger B. (eds) Research in Computational Molecular Biology. RECOMB 2010. Lecture Notes in Computer Science, vol 6044. Springer, Berlin, Heidelberg

Abstract

The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications. We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome. The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the other hand, a novel seeding principle especially adapted to read mapping. Our method can handle both lossy and lossless frameworks and is able to distinguish, at the level of seed design, between SNPs and reading errors. We illustrate our approach by several seed designs and demonstrate their efficiency.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Laurent Noé
    • 1
  • Marta Gîrdea
    • 1
  • Gregory Kucherov
    • 1
  1. 1.INRIA Lille - Nord Europe, LIFL/CNRSUniversité Lille 1Villeneuve d’AscqFrance