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Error correction and diversity analysis of population mixtures determined by NGS

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wood2015peerj645.pdf (1.162Mb)
Date
13/11/2014
Author
Wood, Graham R.
Burroughs, Nigel J.
Evans, David J.
Ryabov, Eugene V.
Keywords
Calibration
Error correction
Honeybee
Metagenome
Nucleotide diversity
Standard sample
Viral mix
QH301 Biology
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Abstract
The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. The error correction method is statistically based and works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated confidence intervals to be calculated. The methods are illustrated using honeybee viral samples. Software in both Excel and Matlab and a guide are available at http://www2.warwick.ac.uk/fac/sci/systemsbiology/research/software/,the Warwick University Systems Biology Centre software download site.
Citation
Wood , G R , Burroughs , N J , Evans , D J & Ryabov , E V 2014 , ' Error correction and diversity analysis of population mixtures determined by NGS ' , PeerJ , vol. 2 , 645 . https://doi.org/10.7717/peerj.645
Publication
PeerJ
Status
Peer reviewed
DOI
https://doi.org/10.7717/peerj.645
ISSN
2167-8359
Type
Journal article
Rights
Copyright 2014 Wood et al. Distributed under Creative Commons CC-BY 4.0
Collections
  • University of St Andrews Research
URI
http://hdl.handle.net/10023/7492

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