piRAT: piRNA Annotation Tool for annotating, analyzing, and visualizing piRNAs

In recent years, Piwi-interacting RNAs (piRNAs) have been found to be involved in different biological roles beyond their initially identified role in protecting the germline genome. However, there is a lack of robust computational tools that facilitate their accurate annotation, analysis, and visualization, which would allow large-scale analysis of piRNAs across samples and species. We present piRAT, a piRNA Annotation Tool for annotating both primary piRNAs from piRNA clusters and secondary piRNAs generated via the ping-pong cycle, using small RNA-seq data mapped to a genome. piRAT also performs descriptive analyses and generates comprehensive reports with visualizations to support annotations and provide further insights. In our comparative analyses, piRAT emerged as the most comprehensive tool available in terms of functionalities. It consistently produced higher-quality annotations of piRNA clusters and ping-pong sites and generated the most detailed reports. As piRAT requires no prior annotations or special data preprocessing, it is a versatile choice for any species, particularly for non-model organisms.