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

[Peter Cock]

On Fri, Mar 9, 2012 at 5:24 PM, Juan Jovel <jovel_juan at hotmail.com> wrote:
>
> 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.

That might work - but you may remove virus reads mapping onto integrated
prophage inside the bacterial etc references you use. Be careful.

Peter