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Error correction and diversity analysis of population mixtures determined by NGS
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Wood, Graham, Burroughs, Nigel John, Evans, David J. and Ryabov, Eugene V. (2014) Error correction and diversity analysis of population mixtures determined by NGS. PeerJ PrePrints, Volume 2 . Article number e645. doi:10.7717/peerj.645 ISSN 2167-9843.
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Official URL: http://dx.doi.org/10.7717/peerj.645
Abstract
The impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees; the methods are illustrated using honeybee viral samples. 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. A statistically based error correction method is presented, which 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. 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.
Item Type: | Journal Article | ||||||
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Subjects: | Q Science > QR Microbiology | ||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||
Library of Congress Subject Headings (LCSH): | Nucleotides, Honeybee, Metagenomics | ||||||
Journal or Publication Title: | PeerJ PrePrints | ||||||
Publisher: | PeerJ, Ltd. | ||||||
ISSN: | 2167-9843 | ||||||
Official Date: | 13 November 2014 | ||||||
Dates: |
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Volume: | Volume 2 | ||||||
Article Number: | Article number e645 | ||||||
DOI: | 10.7717/peerj.645 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||
Date of first compliant deposit: | 28 December 2015 | ||||||
Date of first compliant Open Access: | 28 December 2015 | ||||||
Funder: | Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Great Britain. Department for Environment, Food and Rural Affairs (DEFRA), Natural Environment Research Council (Great Britain) (NERC), Scotland, Wellcome Trust (London, England) | ||||||
Grant number: | BBI0008281 (BBSRC) |
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