Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”

Abstract

Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

“…To elucidate the many facets of recombination and to determine full-length haplotypes of, for example, virus mutants/variants in complex viral populations (quasispecies), long-read sequencing has become the method of choice. Short-read Next-Generation Sequencing technologies (NGS) -such as IonTorrent and Illumina -are restricted by read length (200-400 nucleotides 20 ). For example, the use of inevitably highly fragmented viral RNAs considerably complicates the investigation of haplotypes 21,22 .…”

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

“…To elucidate the many facets of recombination and to determine full-length haplotypes of, for example, virus mutants/ variants in complex viral populations (quasispecies), long-read sequencing has become the method of choice. Short-read secondgeneration sequencing technologies-such as Ion Torrent and Illumina-are restricted by read length (200-400 nt) (Hölzer and Marz 2017). For example, the use of highly fragmented viral RNAs considerably complicates the investigation of haplotypes (Nowak 1992;Baaijens et al 2017).…”

Metagenomics revealing new virus species in farm and pet animals and aquaculture

“…), then trimming (cleavage of adapters, tags, primers), and the alignment and assembly of contigs (mapping to reference sequences or de novo assembly). In general, there are several assembly tools and software (e.g., Geneious, Velvet, and ABySS); but nowadays viral genome specific genome assemblers, such as VICUNA, Viral Assembly Pipeline (VrAP), V-FAT, AV454, RIEMS, and metagenome assemblers like Omega, Genovo, MEGAHIT, MetaSpades, MetaVelvet are also available (Holzer and Marz, 2017; 37 2.5 Bioinformatics Rose et al, 2016;Roy et al, 2018). During de novo assembly, there is no available reference sequence for alignment; this technique is key to identify novel virus genome sequences.…”

“…Commercially available analysis tools (e.g., CLCBIO Genomic Workbench, Avadis NGS, and Softgenetics Nextgene) offer user-friendly solutions for this purpose. Virus-specific data bases are useful to collect relevant information on virus families and also sequence data for subsequent taxonomic and phylogenetic classification (Holzer and Marz, 2017;Kulski, 2016;Rose et al, 2016;Roy et al, 2018). Online platforms are also available to make rapid viral taxonomy in a metagenomic data set [,http://kaiju.binf.ku.dk/.…”