ITS has a rather peculiar behavior in terms of removing the primers from the corresponding sequencing data.
To this end, PEMA implements an extra step in this case, by making use of the
When you are about to run PEMA for ITS data these are the parameters you need to make sure you have ther right:
The next parameters are needed for the
cutadattool. \n You need to set the primers you used there to allow
Regarding the algorithm for ASVs inference or OTU clustering,
you are able to select between the
Swarm and the
We strongly suggest to use the
Swarm option as it scales better and takes less time.