The decontaminate and dereplicate modes work very well and are very fast. I tested them one after the other using GitHub Desktop. I still need to test them with really huge sequence files of hundreds of thousands of small sequences to see where the realistic limits are.
I am just creating this issue here so that we don't forget: Once that Stefanos starts working on the overhauled GUI, we also need to remember to add the possibility of user settings (sequence divergence thresholds etc) to the Decont and Derep modes.
The decontaminate and dereplicate modes work very well and are very fast. I tested them one after the other using GitHub Desktop. I still need to test them with really huge sequence files of hundreds of thousands of small sequences to see where the realistic limits are.
I am just creating this issue here so that we don't forget: Once that Stefanos starts working on the overhauled GUI, we also need to remember to add the possibility of user settings (sequence divergence thresholds etc) to the Decont and Derep modes.