riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data

Abstract

Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies.\n\nAvailability and ImplementationriboWaltz was implemented in R and is available at https://github.com/LabTranslationalArchitectomics/RiboWaltz\n\nContactgabriella.viero@cnr.it or fabio.lauria@unitn.it