CONCUR (Codon counts from Ribo-seq) is a standalone tool for calculating codon usage from Ribo-seq data. CONCUR takes a BAM file with aligned ribosome-protected fragments as input, uses this to estimate the P-site offset per read length and reading frame, and outputs codon counts per ribosome E-, P-, A-site and at flanking positions.
Reference: Frye M and Bornelöv S (2021) CONCUR: quick and robust calculation of codon usage from ribosome profiling data. Bioinformatics 13:3399.
Paper link: https://doi.org/10.1093/bioinformatics/btaa733