PLncFire: A Scalable Pipeline for Transcriptome-wide Discovery of Plant lncRNAs

Long non-coding RNAs (lncRNAs) are key regulators of plant biology, yet their discovery is hindered by low sequence conservation and a lack of comprehensive annotations. To overcome these challenges, we developed PLncFire, a modular computational pipeline that automates the genome-wide identification and annotation of lncRNAs from standard RNA-seq data. PLncFire integrates quality control, transcript assembly, and a robust consensus coding-potential assessment using CPC2, PlantLncPipe, and FEELnc to generate high-confidence predictions. It classifies lncRNAs as known or novel, facilitates their prioritisation through differential expression analysis, and is designed for scalability and reproducibility across diverse plant species. PLncFire provides a standardised framework to empower large-scale lncRNA discovery and advance comparative functional genomics. The source code is available at https://github.com/ahsan-rizvi/PLncFire.git.