How to map viral RNA from human blood samples?

Question

[caggtaagtat]

Hi everyone,

we want to establish a diagnostic tool in our institute of virology, where we extract RNA from a patients blood and than sequence it, maybe following this protocol. I understand everything until I have the reads in this case, however, I don't understand, how I would than map the generated reads.

Can you recommend an aligner for this purpose and where would you get a nice viral genome database? Or do I have to generate a giant fused genome for the alignment ?

Edited the title and the link

Answer 1

[Sej Modha]

DisCVR can do that. It is an app that has been designed specifically to work well within the diagnostic laboratory environment.

[caggtaagtat]

Thank you very much! That's exactly what I was looking for!

[caggtaagtat]

Is it possible to use Nanopore sequencing for that?

[Sej Modha]

I guess as long as the reads are in .fastq format, DisCVR should work, however, I am not sure if it is thoroughly tested with ONT data.