Penguin

Penguin is a tool for predicting pseudouridine sites in direct RNA nanopore sequencing data. The penguin tool needs as input a fast5 path and if you don't provide a sam file you have to provide a reference genome to align to so the tool can create the sam file. If no bed file is provided a default one is included and will be used. The tool will then id all fast5 files and create coordinate file with ids of files that are modified.