Question: Re: Reference Genome
gravatar for tirupathiraobt
2.4 years ago by
tirupathiraobt10 wrote:

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,


bowtie • 635 views
ADD COMMENTlink written 2.4 years ago by tirupathiraobt10
gravatar for vladimir.gritsenko
2.4 years ago by
Tel Aviv University
vladimir.gritsenko90 wrote:

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).

ADD COMMENTlink written 2.4 years ago by vladimir.gritsenko90

How to use a Custom reference genome, if using an existing public Galaxy, including Galaxy Main (

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:

Thanks, Jen, Galaxy team

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Jennifer Hillman Jackson25k
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