Hi Lena,
shouldn’t take that long.
Moreover, we are working on implementing a contamination filter.
You can enable the current version of this using
Edit->Preferences->Enable Software Feature to enter
contaminants
This will allow you to specify one or more contaminant taxa. Note that specifying a higher rank taxon such as e.g. Eukaryota will declare that node and all nodes below it as contaminants.
When this is activated, any read that has a significant alignment to any contaminant taxon will be placed on a special Contamination node.
Please give this new feature a spin and send me your feedback.