Ribo-ODDR: Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs

We have developed the Ribo-ODDR software, a biotinylated oligo design pipeline integrated with a user-friendly interface that assists in oligo selection, to help researchers increase the depth of their Ribo-Seq experiments with efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. In its corresponding publication, we show that Ribo-ODDR designed oligos lead to a significant increase in rRNA depletion, and increased sequencing depth as a result. This is demonstrated with in vivo Ribo-seq experiments performed in mouse colon and in vitro Ribo-seq experiments performed in mouse intestinal organoids. Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR