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PMID: 19668203 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Accurate determination of microbial diversity from 454 pyrosequencing data.

Nature methods ·Vol. 6 ·No. 9 ·2009-09-00 ·Pages 639-41

Quince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT

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.

MeSH Terms
Algorithms Bacteria/genetics Genetic Variation Models, Genetic Polymerase Chain Reaction RNA, Bacterial/genetics RNA, Ribosomal, 16S/genetics Sequence Analysis, DNA/methods Software
Chemicals
RNA, Bacterial RNA, Ribosomal, 16S
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Quince Christopher
Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK. quince@civil.gla.ac.uk
Lanzén Anders
Curtis Thomas P
Davenport Russell J
Hall Neil
Head Ian M
Read L Fiona
Sloan William T
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Article Info
Journal
Nature methods
Abbr.
Nat Methods
ISSN
1548-7105
DOI
10.1038/nmeth.1361
Email
quince@civil.gla.ac.uk
Published
2009-09-00
Epub
2009-00-09
Pages
639-41
Language
English
Region
United States
NLM ID
101215604
Subset
IM
Corrections
CommentIn
PMID: 19718016
External Links
PubMed source DOI: 10.1038/nmeth.1361 View journal details
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