How to find out what genomes are supported in Galaxy? (potato?)

Question: How to find out what genomes are supported in Galaxy? (potato?)

8 weeks ago by

United States

Loraine, Ann • 150 wrote:

Does Galaxy main support any potato genome assemblies? Also, what is the best way to find out which genome versions and assemblies Galaxy supports?

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modified 7 weeks ago by Bjoern Gruening ♦ 5.1k • written 8 weeks ago by Loraine, Ann • 150

8 weeks ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi Ann,

Galaxy can support any genome version. It's just a question if the administrator has installed the genome of interest. Also installing a genome can mean different things. A Galaxy instance, for example, can offer the sequence as a FASTA sequence but might be missing the bowtie2 index. What I want to say is, if you are missing a genome or an index or any support, please get in contact with your Galaxy admin and ask him to install it. Also, please note that you do not need you do not need the installed genome at all. Most of the Galaxy tools support taking a FASTA file from you. So if you have your potato genome, just upload it into your history and you should be good to go. There is also a feature called custom genomes that might help you.

Cheers, Bjoern

ADD COMMENT • link written 8 weeks ago by Bjoern Gruening ♦ 5.1k

8 weeks ago by

Loraine, Ann • 150

United States

Loraine, Ann • 150 wrote:

Follow-up question: Is there a way I can contribute a genome assembly (bowtie index for running alignments, etc) to Galaxy Main so that it would be available "out of the box" for all users?

ADD COMMENT • link written 8 weeks ago by Loraine, Ann • 150

7 weeks ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

We are planning to use this project for this: https://github.com/bgruening/idc But it's not ready for prime-time, you can tell me what you need and I could install it on usegalaxy.eu

ADD COMMENT • link written 7 weeks ago by Bjoern Gruening ♦ 5.1k

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