Accurate determination of microbial diversity from 454 pyrosequencing data

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 f...

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Bibliographic Details
Published inNature methods Vol. 6; no. 9; pp. 639 - 641
Main Authors Quince, Christopher, Lanzén, Anders, Curtis, Thomas P, Davenport, Russell J, Hall, Neil, Head, Ian M, Read, L Fiona, Sloan, William T
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.09.2009
Nature Publishing Group
Subjects
Algorithms
Bacteria - genetics
Bioinformatics
Biological Microscopy
Biological Techniques
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
brief-communication
Deoxyribonucleic acid
DNA
DNA sequencing
Genetic aspects
Genetic Variation
Lakes
Life Sciences
Microbiology
Microorganisms
Models, Genetic
Noise reduction
Nucleotide sequencing
Polymerase Chain Reaction
Proteomics
Research methodology
RNA, Bacterial - genetics
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA - methods
Software
United States
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Summary: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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SourceType-Scholarly Journals-1
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ISSN:1548-7091
1548-7105
DOI:10.1038/nmeth.1361