Recently, we have started to explore the virus’ and host's genomes, transcriptomes, metabolome, proteome, and metagenome but also their phenotype, occurrence, and environment. The biodiversity of viruses with its coverage of multiple scales and its high complexity is a big challenge for algorithm and software development in the big data field ( Beckstein et al., 2014). aĪlthough microorganisms and particularly viruses are tiny, the standard properties of big data apply: volume, variety, velocity, and veracity. “Big data” has been awarded to be the second-best Anglicism in 2014. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Recently, the first specialized virus-bioinformatic organizations have been established. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. We present how viral sequences can be detected de novo out of current short-read NGS data. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. The power of new genome sequencing technologies, associated with new tools to handle “big data”, provides unprecedented opportunities to address fundamental questions in virology. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research.
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