Hi Galaxy team,
I'm Tiru, just started working with Galaxy server. I would like to align my sequences with reference genome. (Clupea harengus (Atlantic herring, Anderson L, et al. 2016)). Could you please update this sequences in galaxy server?.
I look forward to see response.
With regards,
Tiru
You can upload a custom reference as a FASTA file, and most (all?) tools should accept it (you can instruct them to use a reference from the history, as opposed to the local cache).
How to use a Custom reference genome, if using an existing public Galaxy, including Galaxy Main (http://usegalaxy.org).
As an alternative, Data Managers from the Tool Shed could be used, found under a category of the same name, if you want to directly install genomes into a local/cloud Galaxy.
Going forward, we could consider adding the genome to Galaxy Main as a built-in genome/index for tools. Create a request with the exact public source noted (NCBI, UCSC) in this Github ticket: https://github.com/galaxyproject/galaxy/issues/1470
Thanks, Jen, Galaxy team
