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

ABSTRACT: 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, PAPNC) for estimating population diversity from 454 sequence data. The diversity measurements determined using this method were comparable to those calculated by average pairwise difference (APD) of multiply aligned sequences using MEGA5. Diversities were estimated for 9 patient plasma HIV samples s

SUBMITTER: Shao W 

PROVIDER: S-EPMC4104926 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature