Seed design framework for mapping SOLiD reads

Details Seed design framework for mapping SOLiD reads Seed design framework for mapping SOLiD reads

2010-06-14

arxiv.org/abs/1006.2625v1

Research in Computational Molecular Biology, LNBI 6044 : 384-396, 2010

Biology

Quantitative Biology

Quantitative Methods

Scientific paper

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

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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