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:

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

Nature Methods volume 7, pages 668–669 (2010)Cite this article

Subjects

To the Editor:

Pyrosequencing has revolutionized microbial community analysis by allowing the simultaneous assessment of hundreds of microbial communities in multiplex with sufficient depth to resolve meaningful biological patterns. These techniques have been used to study microbial processes on scales ranging from continents1 to within an individual's body2.

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: Comparisons of diversity analyses of filtered to denoised data.

References

  1. Lauber, C.L., Hamady, M., Knight, R. & Fierer, N. Appl. Environ. Microbiol. 75, 5111–5120 (2009).

    Article  CAS  Google Scholar 

  2. Costello, E.K. et al. Science 326, 1694–1697 (2009).

    Article  CAS  Google Scholar 

  3. Caporaso, J.G. et al. Nat. Methods 7, 335–336 (2010).

    Article  CAS  Google Scholar 

  4. Kunin, V., Engelbrektson, A., Ochman, H. & Hugenholtz, P. Environ. Microbiol. 12, 118–123 (2009).

    Article  Google Scholar 

  5. Quince, C. et al. Nat. Methods 6, 639–641 (2009).

    Article  CAS  Google Scholar 

  6. Sogin, M.L. et al. Proc. Natl. Acad. Sci. USA 103, 12115–12120 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank P. Turnbaugh for providing us with an excellent mock community for testing and C. Quince for unpublished insights into how PyroNoise works. J.R. was supported in part by a postdoctoral scholarship from the German Academic Exchange Service (DAAD). This work was supported in part by grants from the US National Institutes of Health, the National Aeronautics and Space Administration and by Howard Hughes Medical Institute.

Author information

Authors and Affiliations

  1. Department of Chemistry & Biochemistry, University of Colorado at Boulder, Boulder, Colorado, USA

    Jens Reeder & Rob Knight

  2. Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado, USA

    Rob Knight

Authors
  1. Jens Reeder
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rob Knight
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rob Knight.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–4, Supplementary Methods (PDF 704 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Reeder, J., Knight, R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 7, 668–669 (2010). https://doi.org/10.1038/nmeth0910-668b

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nmeth0910-668b

This article is cited by

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

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