Assembly of metatranscriptomic data

[Aragion]

Hello.
I have a set of reads produced by metatranscriptomic cDNA sequensing of the total RNA sample. I need to assemble the RNA-virus genome, which was detected in this sample by the RT-PCR-analysis, using some reference sequence from GenBank and the reads. Can you give me some advise on how to perform this task.
Thanks.

[maubp]

You could try a reference guided assembly, perhaps using MIRA?

You might want to first try mapping all the reads against the reference (with relaxed mapping settings) in order to divide the reads into those which might be part of your virus (mapped to the reference) or not (unmapped).