designing efficient spaced seeds for solid read mapping
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ID: 149083
2010
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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.
| Reference Key |
no2010advancesdesigning
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|---|---|
| Authors | ;Laurent Noé;Marta Gîrdea;Gregory Kucherov |
| Journal | journal of hepatocellular carcinoma |
| Year | 2010 |
| DOI |
10.1155/2010/708501
|
| URL | |
| Keywords |
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