Alignment and assembly of metatranscriptomic paired-end reads

[Aragion]

Hello.

I have the sets of metatranscriptomic Illumina paired-end reads. I need to align them against the database of plant virus genomes (about 55000 sequences) and calculate coverage for each reference. How can I solve this problem?
I also want to assemble these reads de novo. I've tried Trinity on Galaxy but the results seem controversial because BLAST search reveals predominantly bacterial and other non-plant viral sequences. May be there are some other online services for metagenomic analysis.