Question: Other reference genomes not listed
gravatar for carlos.cordon
4.0 years ago by
carlos.cordon10 wrote:


I really like Galaxy tool but I have the problem that it does not contain the reference genome of the organism I work with (Trypanosoma brucei). I would like to know if there is any way to load a reference genome not listed in the website. Thanks in advance


customgenomes bowtie genomes • 913 views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by carlos.cordon10
gravatar for Daniel Blankenberg
4.0 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

Hi Carlos,

Most Galaxy tools can use a reference genome in the form of a fasta file uploaded to your history. See for more details.

Thanks for using Galaxy,


ADD COMMENTlink written 4.0 years ago by Daniel Blankenberg ♦♦ 1.7k
gravatar for carlos.cordon
4.0 years ago by
carlos.cordon10 wrote:


Hi Dan,

thanks for your answer. I uploaded the fasta version of my reference desired genome, but still the website tell me that there is not a current genome version of the required format. The fasta version I got it is not probably sorted (it is only the plain text of all bases without sorting it in chromosomes) but I don't know how to sort it properly. Any suggestion?




ADD COMMENTlink written 4.0 years ago by carlos.cordon10


Double check that your dataset is assigned to the datatype "fasta". Also confirm that it is in strict fasta format - there is troubleshooting help in the summary wiki above, and even more in the video and linked-out dedicated wiki page.

Sorting is optional for many tools/pipelines, but if you want to do this or need to (using GATK), convert fasta -> tabular, then use 'Sort', then convert back to fasta. All the tools to do this are in Galaxy: see the groups "Filter and Sort" and "Fasta Manipulation".

You may need to slice the tabular file up (then put it back together) in order to sort properly for GATK, but those tools are also in Galaxy. See the group 'Text Manipulation'. And see the GATK website for how the sorting is expected to be. In short, it is in numerical order, as in the list below. For genomes with alternate chromosome name styles, this can always be a bit confusing, but try something similar, or use the sort order of the reference annotation data you are using (that is known to be GATK compatible).


Best, Jen, Galaxy team

ADD REPLYlink written 4.0 years ago by Jennifer Hillman Jackson25k
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