A novel method for the estimation of diversity in viral populations from next generation sequencing data

A novel method for the estimation of diversity in viral populations from next generation sequencing data
Jean P. Zukurov, Sieberth N. Brito, Luiz M. R. Janini, Fernando Antoneli
Comments: 17 pages, 6 figures, site: this http URL
Subjects: Quantitative Methods (q-bio.QM); Genomics (q-bio.GN)

In this paper we describe the structure and use of a computational tool for the analysis of viral genetic diversity on data generated by high- throughput sequencing. The main motivation for this work is to better understand the genetic diversity of viruses with high rates of nucleotide substitution, as HIV-1 and Influenza. This work focuses on two main fronts: the first is a novel alignment strategy that allows the recovery of the highest possible number of short-reads; the second is the estimation of the populational genetic diversity through a Bayesian approach based on Dirichlet distributions inspired by word count modeling. The software is available as an integrated platform capable of performing all operations described here, it is written in C# (Microsoft) and runs on Windows platforms. The executable, the documentation and the auxiliary files are freely available and may be obtained from: biocomp.epm.br/tanden.

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