[Bioperl-l] Sorry in advance, not exactly a BIOPERL question, but sure you know about it...

[Juan Jovel]

Hello All!
No clear to me what generally speaking is the advantage of filtering out reads when we are interested in de novo assembly of specific taxonomic groups (i.e. bacteria, viruses, fungi, etc). More specifically, my questions are:
1. In a metagenomics library, if I am interested in de novo assembly of virus genomes, should I remove bacterial and human reads (that's what I do), and leave in phages and known viral sequences. 
2. Or should I remove everything what is known and leave only "unknown" reads for assembly??
What are the advantages and pitfalls of each scenario? Thinking in terms of de Bruijn graphs...
Any comment would be highly appreciated and my apologies again.
Cheers,
JUAN