Error correction and diversity analysis of population mixtures determined by NGS

Graham R. Wood*, Nigel J. Burroughs, David J. Evans, Eugene V. Ryabov

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    3 Citations (Scopus)
    4 Downloads (Pure)

    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/, theWarwickUniversity Systems Biology Centre software download site.

    Original languageEnglish
    Article numbere645
    Pages (from-to)1-17
    Number of pages17
    JournalPeerJ
    Volume2
    DOIs
    Publication statusPublished - 2014

    Bibliographical note

    Copyright the Author(s) 2014. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

    Keywords

    • Calibration
    • Error correction
    • Honeybee
    • Metagenome
    • Nucleotide diversity
    • Standard sample
    • Viral mix

    Fingerprint Dive into the research topics of 'Error correction and diversity analysis of population mixtures determined by NGS'. Together they form a unique fingerprint.

    Cite this