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BMC Bioinformatics. 2008 Oct 13;9:431. doi: 10.1186/1471-2105-9-431.

Probabilistic base calling of Solexa sequencing data.

Author information

1
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. jacques.rougemont@epfl.ch

Abstract

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.

PMID:
18851737
PMCID:
PMC2575221
DOI:
10.1186/1471-2105-9-431
[Indexed for MEDLINE]
Free PMC Article

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