Mothur and RDP

Hi everyone,

I’m very very new to analyzing pyrosequencing results. I’m starting to understand how trimming etc. works. A colleague suggested comparing my mothur results to the RDP pyrosequencing pipeline results and here’s where I’m really stuck.

For some reason, although I’m starting with the same fasta file, when I use “trim.seqs” in mothur and use “minlength” and “maxlength” to trim sequences, it gives me a different result then when I set the same initial parameters in RDP. Does anyone have any insight into this?


The RDP uses different parameters for the trim.seqs step. Ours are more stringent (i.e. better) and have been extensively validated and published as described here: