Ribo-Pop

Simple, cost-effective, and widely applicable ribosomal RNA depletion. Snakemake workflow: ribopop_probe_design. This workflow designs oligos that hybridize to rRNA targets. First, a consensus sequence is built for each target. Next, potential probe target sites are screened against the genome and the transcriptome for non-rRNA matches. Finally, probes are selected to cover the targets, while adhering to the specified design parameters and avoiding the predicted non-specific targeting. Snakemake workflow: ribopop_rnaseq. This workflow performs analysis of RNA-Seq data for the Ribo-Pop paper. If you're not using conda, you will need to install snakemake as well as all the other software listed in envs/ribopop_probe_design.yaml in advance of running the workflow using your preferred installation method.