Our ribosome profiling analyses tools are available on github. These include a Nextflow-based preprocessing pipeline as well as a new binary file format for organizing ribosome profiling data as a function of footprint length. This file format leverages hierarchical data format and is akin to binary file formats commonly used in bioinformatics (.bam for sequence alignments, cooler for Hi-C, etc). We also provide a complete R package (riboR), a Python interface (RiboPy) and a command line interface. For beginners, we recommend taking a look at our quick start guide.
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