On the effective depth of viral sequence data.
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Illingworth, C., Roy, S., Beale, M. A., Tutill, H., Williams, R., & Breuer, J. (2017). On the effective depth of viral sequence data.. Virus evolution, 3 (2), vex030. https://doi.org/10.1093/ve/vex030
Genome sequence data are of great value in describing evolutionary processes in viral populations. However, in such studies, the extent to which data accurately describes the viral population is a matter of importance. Multiple factors may influence the accuracy of a dataset, including the quantity and nature of the sample collected, and the subsequent steps in viral processing. To investigate this phenomenon, we sequenced replica datasets spanning a range of viruses, and in which the point at which samples were split was different in each case, from a dataset in which independent samples were collected from a single patient to another in which all processing steps up to sequencing were applied to a single sample before splitting the sample and sequencing each replicate. We conclude that neither a high read depth or a high template number in a sample guarantee the precision of a dataset. Measures of consistency calculated from within a single biological sample may also be insufficient; distortion of the composition of a population by the experimental procedure or genuine within-host diversity between samples may each affect the results. Where it is possible, data from replicate samples should be collected to validate the consistency of short-read sequence data.
Wellcome Trust (101239/Z/13/Z)
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External DOI: https://doi.org/10.1093/ve/vex030
This record's URL: https://www.repository.cam.ac.uk/handle/1810/275402
Attribution 4.0 International
Licence URL: http://creativecommons.org/licenses/by/4.0/
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