Circtools 2.0: a comprehensive framework for enhanced circular RNA bioinformatics

Abstract Background Circular RNAs (circRNAs) play a pivotal role in gene regulation, acting as transcriptional modulators at various cellular levels and exhibit remarkable specificity across cell types and developmental stages. Detecting circRNAs from high-throughput RNA-seq data presents significant challenges, as it requires specialized tools to identify back-splice junctions (BSJ) in raw sequencing data. To address this need, we previously developed circtools , a robust and user-friendly software for circRNA detection, downstream analysis, and wet-lab integration. Results Building on this foundation, we present circtools 2.0 , a major upgrade that pushes the boundaries of computational and experimental workflows in circular RNA research. Key innovations include: (1) an ensemble-based circRNA detection strategy with improved recall, (2) automated circRNA padlock probe design for the Xenium spatial transcriptomics platform, enabling spatial circRNA profiling, (3) cross-species circRNA conservation analysis, and (4) native support for Oxford Nanopore sequencing, allowing full-length circRNA characterization and resolution of internal circRNA structures. Conclusion Circtools 2.0 provides a unified, next-generation platform that substantially broadens the analytical and experimental toolkit for circRNA research. By integrating an ensemble detection strategy, automated padlock probe design, cross-species conservation analysis, and native Oxford Nanopore support, it enables comprehensive, multi-modal interrogation of circRNAs. These advances empower deeper mechanistic studies and open new avenues for understanding the regulatory and functional roles of circRNAs across biological contexts. Availability The source code for circtools 2.0 is available at http://github.com/jakobilab/circtools and licensed under GPLv3.0. The documentation is available at https://docs.circ.tools. Supplementary data are available at BMC online. Graphical abstract