Arabidopsis thaliana TAIR10 genome for HISAT2

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Hi
would it be possible to have the Arabidopsis thaliana TAIR10 genome installed for HISAT2?
thanks a lot
best

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Hello @pej

That genome has not been indexed for HISAT2 at https://usegalaxy.org. We do plan to do that as part of a larger project but it won’t be completed for a bit more time.

You don’t need to wait. There are two choices:

  1. Upload the genome in fasta format and use it as a Custom Reference genome with HISAT2 (and any other tool it is not indexed for) at Galaxy Main https://usegalaxy.org. How-to: Preparing and using a Custom Reference Genome or Build. The exact genome used in Galaxy is here (a good place to source from, since the genome is already indexed for some other tools, and using the same exact genome for all steps in the analysis is very important): http://datacache.galaxyproject.org/
  2. Use the Galaxy EU https://usegalaxy.eu/ server instead, they do have the genome indexed for HISAT2 already.

Thanks!

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