nzhang89/RiboSeeker: A Package for Ribosome Profiling Data Analysis and Visualization

Ribosome profiling is a technology for determining translation activity by sequencing ribosome protected mRNA fragments. We developed RiboSeeker, an end-to-end package for ribosome profiling data analysis. RiboSeeker consists of two main components: data processing and downstream analysis at single nucleotide resolution. The first component was written in Snakemake, a workflow management language, for scalable and reproducible data processing. Taking raw FASTQ reads, the workflow performs adapter sequence trimming, RNA contamination removal, and alignment to a reference genome. Next, starting from an alignment file, a variety of downstream analysis and visualization functionalities were implemented in R, such as read length distribution, genomic feature distribution of aligned reads, and metagene plots. Based on the metagene plots, users can define the desired read length and P-site offset, and further measure the translation of open reading frames (ORFs) by calculating translation efficiency and discover novel ORFs by computing ORFscore. Altogether, RiboSeeker covers the essential data processing and analysis steps for ribosome profiling experiments.

install.packages("remotes")
remotes::install_github("nzhang89/RiboSeeker")