Produce a chimera clean file?

Hey Pat,
Do you think you could include an option that spits out a fasta file that has all chimeric sequences removed. I realize you can apply a filter - but I’d like to just get rid of the chimeras.


The next version of mothur will give you a list sequences that it thinks are chimeric. You can then use this list with remove.seqs to get a file that only contains your good sequences.

In version 1.9, an .accnos file is generated containing the names of chimeric sequences that can be used with the remove.seqs command.