Work

Circtools 2.0: a comprehensive framework for enhanced circular RNA bioinformatics

Year: 2026

Type: article

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.

Source: BMC Bioinformatics

DOI: 10.1186/s12859-026-06517-w

Authors: Shubhada R. Kulkarni, Walker J Compton Mellon, Felix Wiedmann, Constanze Schmidt, Christoph Dieterich, Tobias Jakobi