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2008
- doi: 10.1186/1471-2105-9-431
- issn: 1471-2105
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Vocational guidance--Religious aspects Calling Deoxyribonucleic acid TNA (Nucleic acid) Desoxyribonucleic acid Thymonucleic acidCiter ce document
J. Rougemont et al., « Probabilistic base calling of Solexa sequencing data. », Serveur académique Lausannois, ID : 10.1186/1471-2105-9-431
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BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. RESULTS: We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. CONCLUSION: We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.