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

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.