Seed design framework for mapping SOLiD reads

Laurent Noé 1, 2, * Marta Gîrdea 1, 2 Gregory Kucherov 1, 3
* Corresponding author
2 SEQUOIA2 - Algorithms for large scale sequence analysis
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
3 SEQUOIA - Sequential Learning
LIFL - Laboratoire d'Informatique Fondamentale de Lille, Inria Lille - Nord Europe
Abstract : The advent of high-throughput sequencing technologies con- stituted 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 faith- ful 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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Submitted on : Tuesday, May 18, 2010 - 5:18:56 PM
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Laurent Noé, Marta Gîrdea, Gregory Kucherov. Seed design framework for mapping SOLiD reads. RECOMB, Aug 2010, Lisbon, Portugal. pp.384-396, ⟨10.1007/978-3-642-12683-3_25⟩. ⟨inria-00484642⟩

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