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