E. coli (16S and 23S) and S. cerevisiae (18S and 25S) rRNA benchmark dataset: Samples 1 – 5

Each file named Ecoli&Scerevisiae rRNA Sample-x.tar.xz (x=1-5) contains eight directories 0010, 0050, 0075, 0100, 0200, 0500, 1000 and 2000. Each of these eight directories contains 4+4 subdirectories: Ecoli16S-Ivt, Ecoli23S-Ivt, Scerevisiae18S-Ivt, Scerevisiaes-25S-Ivt/ (in vitro transcripts, no modified sites) Ecoli16S-Native, Ecoli23S-Native, Scerevisiae18S-Native, Scerevisiae25S-Native/ (native transcripts with modified sites) The number of reads in each of these subdirectories corresponds to the name of the parent directory it resides in. All reads were selected from the original dataset Stephenson et al.,Cell Genomics (2022) to approximately span the full reference sequences, resulting in near-uniform coverage depth equal to the directory name (e.g. 10, 50, 75,..,2000). For example, coverage depth for Ecoli&Scerevisiae rRNA Sample-1/0100/Ecoli23S-Ivt-Sample-1 across all reference positions is shown here (note that nearly all position have coverage depth of 100, except at the beginning and the end of the reference sequence). For details about dataset construction either see Vujaklija et al.,Nucleic Acids Research (2024) (Methods section) or drop us an email at [e-mail] rRNA_modifications_Ecoli&Scerevisiae.tsv contains the list of modified sites for E. coli 16S rRNA , E. coli 23S rRNA, S. cerevisiae 18S rRNA and S. cerevisiae 25S. Reads were sequenced with R9.4.1 pore, basecalled with Guppy v.3.1.5 and resquiggled with Tombo v.1.5. For details about the sequencing see Stephenson et al.,Cell Genomics (2022). If you have any questions or would like additional clarification, please feel free to contact me at [e-mail], I’ll be happy to help. If you use this dataset, please cite Vujaklija et al.,Nucleic Acids Research (2024)