miRPipe: Seed-based Synthetic Small Non-coding RNA Sequence Simulator

miRPipe is an end-to-end, modular bioinformatics software designed for accurate detection, annotation, and quantification of small RNAs — including known and novel miRNAs as well as piRNAs — from Next Generation Sequencing (NGS) data. Built with flexibility and reproducibility in mind, miRPipe integrates advanced seed-based clustering and paralogue identification strategies to ensure reliable discovery of unique and functionally related miRNAs. Its performance, validated on synthetic and cancer datasets, demonstrates superior accuracy (95%) and F1-score (94%), making it a powerful and scalable tool for small RNA analysis in research and clinical genomics. GitHub Paper