Dear Perumal

I understand you wish to go for RNA viral NGS analyses.  Please frame question on the kind of parameters like

a. If any, low abundance of viral RNA in relation to host RNA

b. Tissue specifity

There are different methods  where you could detail and methods employed from sequencers like Roche.  This will also allow you to negate methods like ultracentrifugation etc. 

Now comes your bioinformatics part of NGS, there are different OS protocols.  Based on the type of teh file you get, I suggest you use Galaxy or http://viral-ngs.readthedocs.org/en/latest/

Best

Prash 

Hi Perumal,

I think that you are talking about NGS sequence technology. I had worked with the 3 most used platforms (Illumina, Ion and 454) and, for me, Illumina gave the best results related to quality, number of reads and coverage.

Cheers

Dear Perumal,

I had experience with Illumina as well and I have to say that the quality check on reads proved to be quite positive. I advice that. I heard contrasting opinions on PacBioscience instrumentation and I have to say that the Ion chemistry sounds very cool. On the other hand the judgment of Illumina by other collegues was more uniform

Good luck!

NGS is just a method like any other and it's best application depends on the experiment you wish to perform. You're very vague regarding what you want to do. Do you want to simply identify presence/absence of virus or to want to identify the exact strain of virus? Is it a specific, known viruses or novel viruses?

NGS may not be the best approach depending on what the experiment actually is.

Dear Perumal,

As far as I understood you are going to sequence tissue sample that includes viruses. If this is the case, then you will have to assemble reads de novo into contigs after sequencing. This is what defines your choice the most. From my experience you should definitely choose Illumina MiSeq/HiSeq, depending on your particular requirements. You have to avoid Ion Torrent sequencers at all cost because they produce infinite number of false indels that will ruin your de novo assembling. You may also try SOLiD, if Illumina is not an option for you, but if it is possible, use Illumina sequencers because they really produce the best reads.

I agree, definitely choose Illumina MiSeq/HiSeq.

illumina sequencing cause reading accuracy