PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data.

@article{Shao2014PAPNCAN,
  title={PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data.},
  author={Wei Shao and Mary F Kearney and Valerie F. Boltz and Jonathan E. Spindler and John W Mellors and Frank M Maldarelli and John M Coffin},
  journal={Journal of virological methods},
  year={2014},
  volume={203},
  pages={73-80}
}
Estimating viral diversity in infected patients can provide insight into pathogen evolution and emergence of drug resistance. With the widespread adoption of deep sequencing, it is important to develop tools to accurately calculate population diversity from very large datasets. Current methods for estimating diversity that are based on multiple alignments are not practical to apply to such data. In this study, the authors report a novel method (Pairwise Alignment Positional Nucleotide Counting… CONTINUE READING
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