The online workshop E-PAN: Enhancing Pan-Genome Analysis in Plants (May 18th 2026) presented the outcomes of the E-PAN initiative, funded by ELIXIR Commissioned Services: Science tier Biodiversity, food security and pathogens. E-PAN focused on improving and standardising plant pan-genome analysis. With the growth of pan-genome datasets, major challenges remain in quality control, gene presence/absence, structural variant detection, data integration, and visualisation. E-PAN addressed these challenges by defining QC standards, harmonised reporting approaches, and developing practical visualisation solutions. Links to presentations and training materials (video recordings and slides): Welcome and Introduction to E-PAN (Klaas Vandepoele) E-PAN White Paper Overview (Marc Heuermann) Pan-genome QC Tutorial: Practical Guidance and Standards for QC (Pedro Barros) Visualisation Tools: PanBarlex (Patrick König) PLAZA (Michiel Van Bel) KnetMiner (Keywan Hassani-Pak) The workshop aimed at plant pan-genome users, but tool developers, data curators, and other interested researchers may also find this content useful. The session highlighted what has been achieved in the project, where limitations remain, and how the proposed standards and tools can support more reliable and interoperable pan-genome research across plant species.