Parameter: orf-filter easy-taxonomy workflow

[Inge-van-Vugt]

Hi,

I have a question about the parameter orf-filter in the easy-taxonomy workflow.

What is this filter exactly doing? And what is recommended? And is the filter on or off at 0?

Thanks in advance

[milot-mirdita]

The orf filter is the procedure in A2 in the paper:
https://academic.oup.com/view-large/figure/408303786/btab184f1.tif

It works well and speeds up taxonomic annotation of contigs by a lot, however for short reads it can falsely reject reads that otherwise might get a taxonomic label.

[Inge-van-Vugt]

Thanks for the fast reply and the answer, I understand it now!