I have paired-end read samples of possibly strands of bacteria/archaea and maybe even eukaryotes. I am aware of programs like SSU-ALIGN, RNAmmer, and Barrnap. However, I am interested to find similar methods on Galaxy.
On Galaxy, is it possible to find all SSU rRNA (16S/18S) in my samples and then compare those to a comprehensive SSU rRNA tree of prokaryotes/eukaryotes to gain better insight into what may be in this sample?
Thank you for sharing any pipeline advice.