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Error correction and diversity analysis of population mixtures determined by NGS

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Error correction and diversity analysis of population mixtures determined by NGS. / Wood, Graham R.; Burroughs, Nigel J.; Evans, David J.; Ryabov, Eugene V.

In: PeerJ, Vol. 2, 645, 13.11.2014.

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Wood, GR, Burroughs, NJ, Evans, DJ & Ryabov, EV 2014, 'Error correction and diversity analysis of population mixtures determined by NGS' PeerJ, vol. 2, 645. https://doi.org/10.7717/peerj.645

APA

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, 2, [645]. https://doi.org/10.7717/peerj.645

Vancouver

Wood GR, Burroughs NJ, Evans DJ, Ryabov EV. Error correction and diversity analysis of population mixtures determined by NGS. PeerJ. 2014 Nov 13;2. 645. https://doi.org/10.7717/peerj.645

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Wood, Graham R. ; Burroughs, Nigel J. ; Evans, David J. ; Ryabov, Eugene V. / Error correction and diversity analysis of population mixtures determined by NGS. In: PeerJ. 2014 ; Vol. 2.

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@article{2294fce0fdf54c6083b31ce655a346a9,
title = "Error correction and diversity analysis of population mixtures determined by NGS",
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.",
keywords = "Calibration, Error correction, Honeybee, Metagenome, Nucleotide diversity, Standard sample, Viral mix",
author = "Wood, {Graham R.} and Burroughs, {Nigel J.} and Evans, {David J.} and Ryabov, {Eugene V.}",
year = "2014",
month = "11",
day = "13",
doi = "10.7717/peerj.645",
language = "English",
volume = "2",
journal = "PeerJ",
issn = "2167-8359",
publisher = "PEERJ INC",

}

RIS (suitable for import to EndNote) - Download

TY - JOUR

T1 - Error correction and diversity analysis of population mixtures determined by NGS

AU - Wood, Graham R.

AU - Burroughs, Nigel J.

AU - Evans, David J.

AU - Ryabov, Eugene V.

PY - 2014/11/13

Y1 - 2014/11/13

N2 - 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.

AB - 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.

KW - Calibration

KW - Error correction

KW - Honeybee

KW - Metagenome

KW - Nucleotide diversity

KW - Standard sample

KW - Viral mix

U2 - 10.7717/peerj.645

DO - 10.7717/peerj.645

M3 - Article

VL - 2

JO - PeerJ

T2 - PeerJ

JF - PeerJ

SN - 2167-8359

M1 - 645

ER -

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ID: 211241202