Custom database including only specific organisms for reads separation?

[AMK06-1993]

Hi Centrifuge heros,

I searched through the issues and manuals but it's still not clear to me.

I have a mixed metagenomic sample and would like to separate reads that belong to invertebrates/fungi/protoza or any eukaryotic organism (that would also work) from bacteria. Could somebody in a very plain way explain to me how to do it? My plan was to download the CDS of these groups of organisms from NCBI, make it into centrifuge database and then extract reads that mapped and not mapped. However, I have no idea how to start and if it's even possible. Could somebody help? Thank you!

Best,

Witte