Brief Communication | Published:

Accurate determination of microbial diversity from 454 pyrosequencing data

Nature Methods volume 6, pages 639641 (2009) | Download Citation

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Abstract

We present an algorithm, PyroNoise, that clusters the flowgrams of 454 pyrosequencing reads using a distance measure that models sequencing noise. This infers the true sequences in a collection of amplicons. We pyrosequenced a known mixture of microbial 16S rDNA sequences extracted from a lake and found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated.

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Acknowledgements

We thank K. Ashelford (University of Liverpool) for the preliminary bioinformatics analysis of the sequencing data and for making the Mallard code publicly available, S. Huse (Marine Biological Laboratory, Woods Hole) for providing the quickdist algorithm and R. Knight for commenting on the manuscript. C.Q. is supported by a Lord Kelvin Glasgow University fellowship, W.T.S. by an Engineering and Physical Sciences Research Council Advanced Fellowship, R.J.D. by a Royal Society fellowship. The Natural Environment Research Council funded sequencing.

Author information

Affiliations

  1. Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK.

    • Christopher Quince
    •  & William T Sloan
  2. Department of Biology, University of Bergen, Bergen, Norway.

    • Anders Lanzén
  3. School of Civil Engineering and Geosciences, University of Newcastle upon Tyne, Newcastle upon Tyne, UK.

    • Thomas P Curtis
    • , Russell J Davenport
    • , Ian M Head
    •  & L Fiona Read
  4. School of Biological Sciences, University of Liverpool, Liverpool, UK.

    • Neil Hall

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Contributions

T.P.C., R.J.D., I.M.H., C.Q. and W.T.S. designed the study. C.Q. devised algorithms and wrote software. A.L. and C.Q. performed analysis. R.J.D. and L.F.R. performed experiments. N.H. oversaw sequencing. T.P.C., R.J.D., N.H., I.M.H., A.L., C.Q., L.F.R. and W.T.S. wrote the paper.

Corresponding author

Correspondence to Christopher Quince.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figure 1 and Supplementary Tables 1–3

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DOI

https://doi.org/10.1038/nmeth.1361

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