Questions about chimera.uchime

Hello there.

I have a question about how I am removing chimeras from my .fasta file.

I am following Schloss SOP pipeline only in part, and my questions are:

Does it make sense to run the chimera.uchime command against with a .fasta file without any alignment run on it?
It would probably increase the number of chimeras detected or this fact has nothing to do with the working of the command?

Thanks a lot once again

Miguel Ángel

chimera.uchime unaligns everything before starting so the alignment doesn’t matter.

Thank you