Ribosome profiling utilizes Next Generation Sequencing to provide a detailed picture of the protein translation landscape within cells. Cells are lysed, translating ribosomes are isolated, and the ribosome protected mRNA fragments are integrated into a sequencing library. The library is then sequenced and raw data (often in the form of .fastq or .txt files) is generated. This pipeline is flexibly designed to be able to process and perform preliminary analyses on SE (single-end) short (<= 100 bp) read raw sequence data.

See this paper for a recent discussion and detailed protocol of the technique.