Uchime output file names

Hi Pat,
I have a small suggestion. I plan to run both uchime ref and uchime denovo and take the intersection of clean reads (remove anything called chimeric by either method). If mothur gave a unique name to the output of Uchime ref and Uchime denovo, I wouldn’t need to run 1, rename the files and run the second. Also, even if people used only one method, including the name of the method in the outfile name would make it immediately apparent which method was used.

Thank you,
Kathie Mihindukulasuriya

Thanks, that sounds like a good idea. FWIW, we’ve done what you suggest with benchmark datasets and see an increase in the false positive rate with little gain on the false negative rate.