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Probabilistic base calling of Solexa sequencing data | BMC Bioinformatics
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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
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Keywords {đ}
sequencing, base, tags, data, genome, article, pubmed, rolexa, google, scholar, calling, solexa, bases, figure, quality, file, analysis, number, sequence, dna, coverage, intensity, cycle, iupac, intensities, length, channels, cas, image, cutoffs, tag, central, information, reference, score, colony, entropy, function, access, probability, performed, fastq, mapping, authors, research, bioinformatics, full, match, average, files,
Topics {âïž}
high-throughput dna sequencing double-stranded genomic adapters open access article single-stranded dna virus high-throughput data poses solexa/illumina sequencer generates article download pdf high-performance computing facility perform paired-end sequencing high-throughput sequencing information-theoretic base calling enhanced model-based clustering high-throughput techniques high resolution access probabilistic base calling information based metrics construct position-weight matrices long-range pcr amplification[30] full size image designed quality metrics model-based clustering algorithm model-based clustering algorithm[12 dna double helix model-based cluster analysis illumina cluster station arabidopsis methylation patterns[12] illumina software suite sequencing genomic dna paired-end sequencing estimate error rates felix naef high-resolution profiling solexa read mapping dye-specific chemical effects privacy choices/manage cookies error rate defined increased throughput requires short reads assembled common dna variation solexa base calling solexa base-calling large file size probable base calling related subjects de-novo sequencing[9 de-novo sequencing base-pairing contributions authorsâ original file protein-dna interactions[7 t4 dna polymerase
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headline:Probabilistic base calling of Solexa sequencing data
description: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. 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. 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.
datePublished:2008-10-13T00:00:00Z
dateModified:2008-10-13T00:00:00Z
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Base Calling
Solexa Sequence
Estimate Error Rate
Probability Simplex
IUPAC Code
Bioinformatics
Microarrays
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Algorithms
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headline:Probabilistic base calling of Solexa sequencing data
description: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. 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. 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.
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Base Calling
Solexa Sequence
Estimate Error Rate
Probability Simplex
IUPAC Code
Bioinformatics
Microarrays
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Algorithms
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