Probabilistic base calling of Solexa sequencing data.
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.


CONCLUSIONS
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.
Rougemont
Jacques
J
School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland. jacques.rougemont@epfl.ch
Amzallag
Arnaud
A
Iseli
Christian
C
Farinelli
Laurent
L
Xenarios
Ioannis
I
Naef
Felix
F
D010584:Bacteriophage phi X 174 / Q000235:genetics; D001483:Base Sequence / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D016000:Cluster Analysis; D004279:DNA, Viral / Q000032:analysis*; D020224:Expressed Sequence Tags; D010363:Pattern Recognition, Automated / Q000379:methods; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013050:Spectrometry, Fluorescence / Q000379:methods
D004279:DNA, Viral