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 found that without noise reduction the number of operational taxonomic units is overestimated but using PyroNoise it can be accurately calculated.
Quince
Christopher
C
Department of Civil Engineering, Rankine Building, University of Glasgow, Glasgow, UK. quince@civil.gla.ac.uk
Lanzén
Anders
A
Curtis
Thomas P
TP
Davenport
Russell J
RJ
Hall
Neil
N
Head
Ian M
IM
Read
L Fiona
LF
Sloan
William T
WT
D000465:Algorithms; D001419:Bacteria / Q000235:genetics*; D014644:Genetic Variation; D008957:Models, Genetic; D016133:Polymerase Chain Reaction; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S