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Diversity Analysis in Viral Metagenomes

  • Jorge Francisco Vázquez-Castellanos
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1838)

Abstract

Viruses are the most abundant and diverse biological entity in the earth. Nowadays, there are several viral metagenomes from different ecological niches which have been used to characterize new viral particles and to determine their diversity. However, viral metagenomic data have the disadvantage to be high-dimensional compositional and sparse. This type of data renders many of the conventional multivariate statistical analyses inoperative. Fortunately, different libraries and statistical packages have been developed to deal with this problem and perform the different ecological and statistical analyses. In the present chapter, it is analyzed simulated viral metagenomes, based on real human gut-associated viral metagenomes, using different R and python packages. The example presented here includes the estimation and comparison of different indexes of diversity, evenness, and richness; perform different ordination and statistical analysis using different dissimilarity metrics; determine the optimal cluster configuration and perform biomarker discovery. The scripts and the simulated datasets are in https://github.com/jorgevazcast/Viromic-diversity

Key words

Ordination analysis Viral metagenomics Alpha diversity Beta diversity Clustering and biomarker discovery 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Jorge Francisco Vázquez-Castellanos
    • 1
  1. 1.Department of Genomics and HealthFundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (Fisabio)ValenciaSpain

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