Expanding the built-in reference genomes

Hi, I am a scientist working on Chlamydia infections. It would be very helpful for the Chlamydia community to add a few Chlamydiae reference genomes to Galaxy’s in-built reference genomes. Would you please let me know if this is something that I can do as a user or if I need to get in touch with the Galaxy team for it?
Thanks, Ehsan

Welcome, @eghasemi

The fastest way to incorporate this reference genome at the EU, AU or ORG servers (and many others) is to use it as a custom reference genome. That can be promoted to a custom build to create a custom database “metadata” key that can be assigned to datasets as needed. The input is a simple fasta file. Make sure to get the matching reference annotation at the same time to avoid problems later on.

This prior Q&A has links to the “how-to”. You can click on the tags to find more examples in different contexts. → Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at - #2 by jennaj

The EU server admins can also comment, but as far as I know, new reference genomes will be indexed sometime later this year for all three UseGalaxy.* servers.

If you want to post back the exact link to the reference genome version(s) you are interesting in working with, we keep track of requests for incorporation later on. Public sources are best: NCBI SRA and UCSC are two examples.

Hope that helps!


Hi @eghasemi

We have a brand new way (since yesterday!) to incorporate reference data, and I’d like to test it out with your reference genomes. So, please do send back which data is involved if this interests you. The custom methods are always valid – but if we can support your community even more with native indexes, I’d like to give that a try too.