Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Correspondence
  • Published:

Intensity normalization improves color calling in SOLiD sequencing

Nature Methods volume 7, pages 336–337 (2010)Cite this article

Subjects

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 subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Effect of normalization on color proportions and SNP calling.

References

  1. McKernan, K.J., et al. Genome Res. 19, 1527–1541 (2009).

    Article  CAS  Google Scholar 

  2. Tang, F. et al. Nat. Methods 6, 377–382 (2009).

    Article  CAS  Google Scholar 

  3. Bravo, H.C. & Irizarry, R.A. Biometrics advance online publication, 13 November 2009 (doi: 10.1111/j.1541-0420.2009.01353.x).

    Article  Google Scholar 

  4. Quinlan, A.R., Stewart, D.A., Stromberg, M.P. & Marth, G. Nat. Methods 5, 179–181 (2008).

    Article  CAS  Google Scholar 

  5. Kao, W.C., Stevens, K. & Song, Y.S. Genome Res. 19, 1884–1895 (2009).

    Article  CAS  Google Scholar 

  6. Hayden, E.C. Nature 451, 378–379 (2008).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA

    Hao Wu, Rafael A Irizarry & Héctor Corrada Bravo

Authors
  1. Hao Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rafael A Irizarry
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Héctor Corrada Bravo
    View author publications

    You can also search for this author in PubMed 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:

  • DOI: https://doi.org/10.1038/nmeth0510-336

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing