Hi all, I'm currently working on a project that requires processing NGS data using custom reference genomes not available in the public Galaxy reference database. I've been exploring different ways to upload and use these genomes efficiently within workflows. My questions: What’s the recommended method for integrating custom genomes into Galaxy? Are there best practices for indexing (e.g., BWA, Bowtie2) to ensure compatibility across tools? Can these genomes be shared across users in a Galaxy instance or history? Any documentation links or example workflows would be highly appreciated. Thanks in advance for your guidance! Best, https://grannygame.org/