PEMA investigating metabarcoding

ITS analysis

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 cutadapt tool.

When you are about to run PEMA for ITS data these are the parameters you need to make sure you have ther right:

  • gene gene_ITS

The next parameters are needed for the cutadat tool. \n You need to set the primers you used there to allow cutadapt to perform



Regarding the algorithm for ASVs inference or OTU clustering, you are able to select between the Swarm and the CROP algorithms.

We strongly suggest to use the Swarm option as it scales better and takes less time.