Introduction

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.

Publications

  1. Designing Efficient Spaced Seeds for SOLiD Read Mapping.
    Cite this
    Noé L, Noé L, Gîrdea M, Kucherov G, 2010-01-01 - Advances in bioinformatics

Credits

  1. Laurent Noé
    Developer

  2. Laurent Noé
    Developer

  3. Marta Gîrdea
    Developer

  4. Gregory Kucherov
    Investigator

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Summary
AccessionBT000698
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC
User InterfaceTerminal Command Line
Download Count0
Submitted ByGregory Kucherov