All Code underlaying the discovery of theta ribozymes: https://www.nature.com/articles/s41467-024-45653-w
The following packages and external software was used for the analysis:
The following existing/external software was used, though other versions may work:
genomad v1.3.3, RNArobo v2.1.0, tRNAscan-SE v2.0.9, Python v.3.7.6, Prodigal v2.6.3, WordCloud v1.5.0, R2R v1.0.6, pandas v1.0.3, NumPy v.1.18.1, Jupyterlab v3.5.0
The whole workflow is split into 3 major sections:
-Databases for all analysis in annotated databases, motif improvement, taxonomic assignments, coding density and code usage analysis.
-Metagenomic for all analysis on raw reads from over 400000 metagenomic samples.
-Combined: Combining all files to the final tables (S1 and S2), including analysis for unique number of ribozymes, sorting and naming of them.