Intensity normalization improves color calling in solid sequencing

Access through your institution Buy or subscribe To the Editor: Applied Biosystems' SOLiD system1 is a commonly used massively parallel DNA sequencing platform for applications from

genotyping and structural variation analysis1 to transcriptome quantification and reconstruction2. Like other sequencing technologies, it measures fluorescence intensities from dye-labeled

molecules to determine the sequence of DNA fragments. Ultimately, sequences are determined by complicated statistical manipulations of noisy intensity measurements, and systematic biases may

mislead downstream analysis3. Several proposed methods improve base calling and quality metrics for other sequencing technologies3,4,5, and we now present Rsolid, software implementing an

intensity normalization strategy for the SOLiD platform that substantially improves yield and accuracy at small computational costs (6% increase in total matches, 13% increase in perfect

matches, 5% reduced error rate and a substantial reduction in false positive single-nucleotide polymorphism (SNP) calls in an _Escherichia coli_ genomic DNA sample). This is a preview of

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about institutional subscriptions * Read our FAQs * Contact customer support REFERENCES * McKernan, K.J., et al. _Genome Res._ 19, 1527–1541 (2009). Article  CAS  Google Scholar  * Tang, F.

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references AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA Hao Wu, Rafael A Irizarry 

& Héctor Corrada Bravo Authors * Hao Wu View author publications You can also search for this author inPubMed Google Scholar * Rafael A Irizarry View author publications You can also

search for this author inPubMed Google Scholar * Héctor Corrada Bravo View author publications You can also search for this author inPubMed Google Scholar CORRESPONDING AUTHORS

Correspondence to Hao Wu or Héctor Corrada Bravo. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial interests. SUPPLEMENTARY INFORMATION SUPPLEMENTARY TEXT

AND FIGURES Supplementary Figure 1, Supplementary Tables 1–4, Supplementary Methods (PDF 1021 kb) RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Wu, H.,

Irizarry, R. & Bravo, H. Intensity normalization improves color calling in SOLiD sequencing. _Nat Methods_ 7, 336–337 (2010). https://doi.org/10.1038/nmeth0510-336 Download citation *

Issue Date: May 2010 * DOI: https://doi.org/10.1038/nmeth0510-336 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a

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