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dc.contributor.authorWood, Graham R.
dc.contributor.authorBurroughs, Nigel J.
dc.contributor.authorEvans, David J.
dc.contributor.authorRyabov, Eugene V.
dc.date.accessioned2015-09-16T16:10:03Z
dc.date.available2015-09-16T16:10:03Z
dc.date.issued2014-11-13
dc.identifier.citationWood , 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.645en
dc.identifier.issn2167-8359
dc.identifier.otherPURE: 211241202
dc.identifier.otherPURE UUID: 2294fce0-fdf5-4c60-83b3-1ce655a346a9
dc.identifier.otherWOS: 000347625900002
dc.identifier.otherScopus: 84911400347
dc.identifier.urihttp://hdl.handle.net/10023/7492
dc.description.abstractThe 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.
dc.format.extent17
dc.language.isoeng
dc.relation.ispartofPeerJen
dc.rightsCopyright 2014 Wood et al. Distributed under Creative Commons CC-BY 4.0en
dc.subjectCalibrationen
dc.subjectError correctionen
dc.subjectHoneybeeen
dc.subjectMetagenomeen
dc.subjectNucleotide diversityen
dc.subjectStandard sampleen
dc.subjectViral mixen
dc.subjectQH301 Biologyen
dc.subject.lccQH301en
dc.titleError correction and diversity analysis of population mixtures determined by NGSen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.School of Biologyen
dc.contributor.institutionUniversity of St Andrews.Biomedical Sciences Research Complexen
dc.identifier.doihttps://doi.org/10.7717/peerj.645
dc.description.statusPeer revieweden


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