Hi guys!
I just have a doubt that why we conduct alignment before classification, as before I consulted a similar question to a RDP staff and he told me that “The alignment is NOT needed for RDP Classifier to make assignment. It would be better off just use your raw reads for the classification.” Because after alignment and filtering in mothur, the sequence length will reduce and then the result of classification will not be so accurate as using the raw reads. So should we firstly reduce sequence errors, the do classification and at last do alignment? Thank you very much!