SV-EViz: a user-friendly web platform for structural variant evaluation and visualization

Recent advances in high-throughput sequencing technologies and computational genomics have substantially expanded our ability to characterize large-scale genomic variation. Within this landscape, structural variants (SVs) constitute a particularly impactful class of variation. Unlike small variants such as single-nucleotide polymorphisms (SNPs) or short insertions and deletions (indels), SVs often span thousands of base pairs and can exert widespread effects on gene structure, regulation, and downstream biological pathways. Despite their biological relevance, reliable detection and interpretation of SVs remain challenging due to fundamental differences in algorithmic assumptions, breakpoint definitions, and matching criteria across SV callers. Furthermore, the absence of a universally accepted definition of SV equivalence prevents the establishment of a single gold-standard benchmarking tool. Consequently, achieving concordance among SV callsets has become a critical requirement for robust and reproducible genomic analyses. Moreover, generating SV consensus and benchmarking often requires switching between different tools, different parameter structures, different file formats, and different output types. Even though command-line tools remain fundamental and indispensable in bioinformatics, researchers who work primarily at the biological interpretation level and require non-automated, exploratory inspection of SV benchmarking outputs may find the fragmented multi-tool structure challenging to navigate. SV-EViz is designed for this context: supporting researchers who need to configure, run, and inspect SV benchmarking results interactively, without requiring scripting expertise or pipeline infrastructure. To address these challenges, this study introduces a novel web-based platform designed to streamline the SV analysis workflow. SV-EViz combines consensus generation, benchmarking, metric harmonization with visualization in a single platform. Widely used command-line tools, including SURVIVOR, EvalSVcallers, and Truvari, are integrated into an intuitive interface that enables in-depth exploration of comparison results through interactive visualizations such as Sankey diagrams, Circos plots, Clustergrams, and Manhattan plots. In addition, it automatically produces structured tabular summaries of key performance metrics—including precision, recall, and F1-score—stratified by SV type, allowing users to evaluate results efficiently and transparently. The platform is offered as a self-hosted web application, with a publicly hosted web version on Render; for local or server-based installations, the source code and Docker-based deployment files are available via the GitHub repository. SV-EViz is a structured platform that allows users to interpret the outputs of existing benchmarking tools through common tables and visualizations, without altering the matching logic of these tools. By unifying SV comparison, performance evaluation, and advanced visualization within a single platform, SV-EViz reduces technical barriers, simplifies analytical workflows, and provides reproducible and interpretable genomic analyses for researchers.