RDG
Python implementation of Ribosome Decision Graphs. Build and analyze RDG representations of translated loci from GTF annotations and Ribo-Seq data.
Tools
Open-source software for analyzing ribosome profiling data and genome annotation. All tools are available on GitHub.
Data Structures & Analysis
TranslonScorer
Command-line implementation of the Trips-Viz ORF calling method. Identify and score translated regions from ribosome profiling data.
Quality Control & Processing
RiboMetric
Comprehensive quality assessment for Ribo-Seq datasets. Generates reports using standalone metrics that don't require reference comparisons.
Collapse-FASTQ
Fetch FASTQ files, clean reads, and collapse PCR duplicates. Preprocessing tool for Ribo-Seq data.
get-RPF
Extract ribosome-protected fragments (RPFs) from Ribo-Seq reads. Utility for isolating the signal from raw sequencing data.
Workflows
PhyloCSF-nf
Nextflow pipeline for running PhyloCSF on candidate coding regions. Evaluates evolutionary conservation signatures of protein-coding potential.
Resources
awesome-riboseq
A curated list of bioinformatic tools for working with Ribo-Seq data. Community resource covering alignment, quantification, visualization, and analysis tools.