Hi Sathish,

Please note that both the technologies are for different application. For a known virus (for which you have PCR primers)  you have to amplify a region of the virus by PCR, followed by direct sanger sequencing or sequencing after cloning. For viruses cloning is better before going for a Sanger sequencing, since viruses are often present in the host as a quasispecies.

However, for unknown templates, you can use the Ion Torrent platform or any other NGS. different NGS platforms require different amounts of template, roughly 1-2 ug. since getting this much of viral template is not possible for clinical samples or field samples, you have to follow host genetic material depletion procedure followed by viral template enrichment through non-specific amplification to get better S/N ratio and meaningful results in NGS experiments. 

best wishes,

SD