Reconstructing rRNA 16S in E.coli frm ribo-seq data

Question

[davide.chiarugi]

I would like to find the variants of the ribosomal RNA 16S in E.coli analysing data coming from ribo-seq (or RNA-seq) experiments. The approach I'm trying consist in reconstructing de novo the rRNA 16S from the (single end) reads coming from a given ribo-seq experiments and see how many rRNA variants comes out. Could anyone suggest me a software that is sensitive enough for this kind of analysis ?

Thanks in advance !