{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T18:16:20Z","timestamp":1787940980413,"version":"build-2784847793"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T00:00:00Z","timestamp":1785283200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>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, 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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 outputs, or running an integrated workflow to produce and visualize SVs on the fly.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/synflow.southgreen.fr; source code https:\/\/github.com\/SouthGreenPlatform\/synflow; preprocessing Snakemake workflow https:\/\/gitlab.cirad.fr\/agap\/cluster\/snakemake\/synflow.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag567","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T11:15:53Z","timestamp":1785237353000},"source":"Crossref","is-referenced-by-count":0,"title":["SynFlow: an interactive online genome structural variant viewer"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9308-974X","authenticated-orcid":false,"given":"Marilyne","family":"Summo","sequence":"first","affiliation":[{"name":"UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier 34398,","place":["France"]},{"name":"CIRAD, UMR AGAP Institut , Montpellier 34398,","place":["France"]},{"name":"South Green Bioinformatics Platform, French Institute of Bioinformatics (IFB); Bioversity; CIRAD; INRAE; IRD , Montpellier 34398,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ga\u00ebtan","family":"Droc","sequence":"additional","affiliation":[{"name":"UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier 34398,","place":["France"]},{"name":"CIRAD, UMR AGAP Institut , Montpellier 34398,","place":["France"]},{"name":"South Green Bioinformatics Platform, French Institute of Bioinformatics (IFB); Bioversity; CIRAD; INRAE; IRD , Montpellier 34398,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0284-1885","authenticated-orcid":false,"given":"Mathieu","family":"Rouard","sequence":"additional","affiliation":[{"name":"South Green Bioinformatics Platform, French Institute of Bioinformatics (IFB); Bioversity; CIRAD; INRAE; IRD , Montpellier 34398,","place":["France"]},{"name":"Bioversity International, Parc Scientifique Agropolis II , Montpellier 34397,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5179-972X","authenticated-orcid":false,"given":"Gautier","family":"Sarah","sequence":"additional","affiliation":[{"name":"UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro , Montpellier 34398,","place":["France"]},{"name":"South Green Bioinformatics Platform, French Institute of Bioinformatics (IFB); Bioversity; CIRAD; INRAE; IRD , Montpellier 34398,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,29]]},"reference":[{"key":"2026082813180357900_btag567-B1","doi-asserted-by":"publisher","DOI":"10.1101\/2025.01.15.633221","article-title":"ntSynt-viz: visualizing synteny patterns across multiple genomes","author":"Coombe","year":"2025","journal-title":"bioRxiv"},{"key":"2026082813180357900_btag567-B2","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1186\/s13059-023-02914-z","article-title":"JBrowse 2: a modular genome browser with views of synteny and structural variation","volume":"24","author":"Diesh","year":"2023","journal-title":"Genome Biol"},{"key":"2026082813180357900_btag567-B3","doi-asserted-by":"publisher","first-page":"2922","DOI":"10.1093\/bioinformatics\/btac196","article-title":"Plotsr: visualizing structural similarities and rearrangements between multiple genomes","volume":"38","author":"Goel","year":"2022","journal-title":"Bioinformatics"},{"key":"2026082813180357900_btag567-B4","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1186\/s13059-019-1911-0","article-title":"SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies","volume":"20","author":"Goel","year":"2019","journal-title":"Genome Biol"},{"key":"2026082813180357900_btag567-B5","doi-asserted-by":"publisher","DOI":"10.1101\/2024.05.09.593317","article-title":"SYNY: a pipeline to investigate and visualize collinearity between genomes","author":"Julian","year":"2024","journal-title":"bioRxiv"},{"key":"2026082813180357900_btag567-B6","doi-asserted-by":"publisher","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake\u2014a scalable bioinformatics workflow engine","volume":"28","author":"K\u00f6ster","year":"2012","journal-title":"Bioinformatics"},{"key":"2026082813180357900_btag567-B7","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2026082813180357900_btag567-B8","doi-asserted-by":"publisher","first-page":"2447","DOI":"10.1038\/s41467-024-46614-z","article-title":"Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data","volume":"15","author":"Liu","year":"2024","journal-title":"Nat Commun"},{"key":"2026082813180357900_btag567-B9","doi-asserted-by":"publisher","first-page":"e1005944","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: a fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2026082813180357900_btag567-B10","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1038\/s41467-025-56329-4","article-title":"Unravelling genomic drivers of speciation in Musa through genome assemblies of wild banana ancestors","volume":"16","author":"Martin","year":"2025","journal-title":"Nat Commun"},{"key":"2026082813180357900_btag567-B11","doi-asserted-by":"publisher","first-page":"btaf332","DOI":"10.1093\/bioinformatics\/btaf332","article-title":"SVbyEye: a visual tool to characterize structural variation among whole-genome assemblies","volume":"41","author":"Porubsky","year":"2025","journal-title":"Bioinformatics"},{"key":"2026082813180357900_btag567-B12","doi-asserted-by":"publisher","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btag567\/70351791\/btag567.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/8\/btag567\/70351791\/btag567.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/42\/8\/btag567\/70351791\/btag567.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T17:18:06Z","timestamp":1787937486000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btag567\/8746885"}},"subtitle":[],"editor":[{"given":"Jianlin","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,7,29]]},"references-count":12,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btag567","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,8]]},"published":{"date-parts":[[2026,7,29]]},"article-number":"btag567"}}