Ribo-Pop

Ribo-Pop performs antisense oligo design and probe selection to deplete ribosomal RNA (rRNA) prior to RNA-Seq library construction, enabling more comprehensive transcriptome sequencing.

Key Features:

• Open-Source Accessibility: Provides an open-source workflow and antisense oligo design strategy that can be adapted for any organism with a sequenced genome.
• Broad Applicability: Designed to operate across a wide range of RNA input levels and multiple species, addressing limitations of species-specific proprietary methods.
• Probe Selection Pipeline: Implements a computational pipeline that builds consensus sequences for rRNA targets, screens potential probe sites against the genome and transcriptome to avoid non-rRNA matches, and selects probes that meet specified design parameters while minimizing non-specific targeting.
• Streamlined Protocol: Supplies a 20-minute laboratory protocol and ready-to-use oligo sequences for several organisms.
• Comprehensive Transcriptome Representation: Depletes rRNA rather than relying on poly(A) selection to retain non-polyadenylated and broader RNA species in RNA-Seq libraries.

Scientific Applications:

• Comprehensive RNA abundance measurement: Enables quantification of diverse RNA species by reducing rRNA contamination in sequencing libraries.
• Non-model and diverse organism studies: Adapts oligo design to any sequenced genome, facilitating transcriptome analysis in non-model organisms.
• RNA-Seq workflow optimization: Improves the quality and comprehensiveness of RNA-Seq results by decreasing rRNA-derived reads.

Methodology:

Ribo-Pop provides two Snakemake workflows: ribo-pop_probe_design, which constructs consensus sequences for rRNA targets, screens candidate probe sites against the genome and transcriptome, and selects probes based on coverage and design parameters while avoiding non-specific interactions; and ribo-pop_rnaseq, which analyzes RNA-Seq data to assess depletion and sequencing outcomes.