Next-generation sequencing in clinical virology: Discovery of new viruses

Table 2 Important bioinformatics challenges associated with application of next-generation sequencers in viral diagnostics action taken or proposed to overcome challenges

Bioinformatics challenges associated with application of NGS in viral diagnostics	Action taken or proposed to overcome challenges
Generation of huge volumes of data by NGS platforms-“data deluge”	Advancement in storage and computation facilities, availability of computer with greater storage and highly powerful processors, cluster/grid computing and cloud computing. Computation facilities needs to be updated with emergence of newer platforms delivering larger datasets
Challenges in uploading data for submission to databases and supercomputing servers for analysis	Requirement of uninterrupted and extremely fast networks
Challenges in storage, public archival and ease of access	Creation of specialized data archive such as the Sequence Read Archive by NIH and ENA (European nucleotide Archive) by EBI. Sharing of data within the three major databases (NIH, EBI and DDBJ) for public accessibility
Challenges in analysis and visualization of large volumes of data, beyond the scope of computation facilities available in molecular biology laboratories	Creation of metagenomic or NGS data analysis pipelines and integrated tool kits, such as those available at NIH-NCBI, EMBL-EBI, MGRAST, CASAVA, MetaVir, Megan, UCSC Genome Browser, BioLinux, etc., availability of cloud computing based servers such as Galaxy
Challenges in alignment, de novo assembly, gene prediction and phylogenetic analyses NGS datasets, especially short read datasets	Availability of alignment algorithms/programs such as ABySS, ELAND, SOAP, Bowtie, Cloudburst, Zoom, BWA, SHRiMP, MOM, SeqMap, Metagene, Velvet, QSRA, ALLPATHS, EDENA, VCAKE, FragGeneScan, BLAST, GLIMMER, EULER-SR, Avadis, Eagle View, etc.
Interpretation of huge amount of data generated in metagenomic analyses by NGS platforms	Proper interpretation of analyzed data is of utmost importance to identify newer pathogens as well as their clinical significance

NGS: Next-generation sequencers.