SynFlow: an interactive online genome structural variant viewer

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ID: 322771
2026
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Abstract
Abstract Motivation Structural variations (SVs), including inversions, translocations, duplications, and large insertions or deletions, are key drivers of genome evolution and phenotypic diversity. With the increasing number of high-quality, chromosome-scale genome assemblies, the ability to detect and interpret SVs has become a crucial aspect of modern genomics. While SV detection has advanced, most visualization methods produce static plots that fall short when researchers, particularly in comparative genomics, need to interactively explore large datasets, zoom into specific genomic regions, or dynamically filter structural events in real time. Results To address this gap, we introduce SynFlow, a lightweight, web-based interactive application specifically designed for exploring and visualizing structural variations identified by SyRI. We demonstrate that SynFlow can reproduce complex static synteny plots published in literature, but transforms them into dynamic, shareable visualizations that support real-time filtering, reordering, and deep exploration of specific SVs, including translocations. SynFlow is available as a web server and offers multiple entry points: browsing precomputed datasets (e.g., banana and grapevine genomes), uploading user-provided SyRI outputs, or running an integrated workflow to produce and visualize SVs on the fly. Availability https://synflow.southgreen.fr; source code https://github.com/SouthGreenPlatform/synflow; preprocessing Snakemake workflow https://gitlab.cirad.fr/agap/cluster/snakemake/synflow. Supplementary information Supplementary data are available at Bioinformatics online.
Reference Key
openalex_W7171699185 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Marilyne Summo, Gaëtan Droc, Mathieu Rouard, Gautier Sarah
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag567
URL
https://doi.org/10.1093/bioinformatics/btag567
Keywords Keywords not found

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