SynFlow: an interactive online genome structural variant viewer

Abstract

Motivation: Structural variations (SVs), including inversions, translocations (TRAs), duplications, and large insertions or deletions, are key drivers of genome evolution and phenotypic diversity. With the increasing number of high-quality, chro- mosome-scale genome assemblies, the ability to detect and interpret SVs has become a crucial aspect of modern geno- mics. 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 SVs 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 TRAs. 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 out- puts, or running an integrated workflow to produce and visualize SVs on the fly. Availability and implementation: https://synflow.southgreen.fr; source code https://github.com/SouthGreenPlatform/syn flow; preprocessing Snakemake workflow https://gitlab.cirad.fr/agap/cluster/snakemake/synflow.

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BibTeX RIS

BibTeX

@article{summo2026synflow,
  title = {{SynFlow: an interactive online genome structural variant viewer}},
  author = {Marilyne Summo and Gaëtan Droc and Mathieu Rouard and Gautier Sarah},
  journal = {Bioinformatics},
  year = {2026},
  month = jul,
  doi = {10.1093/bioinformatics/btag567},
  url = {https://hal.science/hal-05735103v1},
  note = {CC BY 4.0},
}

RIS

TY  - JOUR
TI  - SynFlow: an interactive online genome structural variant viewer
AU  - Marilyne Summo
AU  - Gaëtan Droc
AU  - Mathieu Rouard
AU  - Gautier Sarah
PY  - 2026
DA  - 2026/07/29
JO  - Bioinformatics
DO  - 10.1093/bioinformatics/btag567
UR  - https://hal.science/hal-05735103v1
AB  - Motivation: Structural variations (SVs), including inversions, translocations (TRAs), duplications, and large insertions or deletions, are key drivers of genome evolution and phenotypic diversity. With the increasing number of high-quality, chro- mosome-scale genome assemblies, the ability to detect and interpret SVs has become a crucial aspect of modern geno- mics. 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 SVs 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 TRAs. 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 out- puts, or running an integrated workflow to produce and visualize SVs on the fly. Availability and implementation: https://synflow.southgreen.fr; source code https://github.com/SouthGreenPlatform/syn flow; preprocessing Snakemake workflow https://gitlab.cirad.fr/agap/cluster/snakemake/synflow.
SN  - 1367-4803
SN  - 1367-4811
ER  -

Abstract

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