# How to bring the reference genome to Usegalaxy

**URL:** https://help.galaxyproject.org/t/how-to-bring-the-reference-genome-to-usegalaxy/4999
**Category:** Uncategorized
**Tags:** troubleshooting, reference-genome, usinggalaxy
**Created:** [December 11, 2020, 2:01pm UTC](https://help.galaxyproject.org/t/how-to-bring-the-reference-genome-to-usegalaxy/4999 "2020-12-11T14:01:18Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![agrieng3](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/agrieng3/32/378_2.png) [@agrieng3](https://help.galaxyproject.org/u/agrieng3)
#### Post date: [December 11, 2020, 2:01pm UTC](https://help.galaxyproject.org/t/how-to-bring-the-reference-genome-to-usegalaxy/4999/1 "2020-12-11T14:01:18Z")

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How to bring the reference genome bovine to Usegalaxy for use in GATK, **Variant Recalibrator**  
there are not “bovine” reference genome in **Variant Recalibrator**.  
I bring refseq with UCSC but i think sth is wrong and **Variant Recalibrator** done with error!  
I did it in UCSC as below:  
UCSC/genome:Cow/select the assembly then group:Mapping and Sequencing, Track Assembly/ last **output format:** = “sequence” and get output to Galaxy

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### Author: ![innovate-invent](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/innovate-invent/32/734_2.png) [@innovate-invent](https://help.galaxyproject.org/u/innovate-invent)
#### Post date: [December 11, 2020, 5:03pm UTC](https://help.galaxyproject.org/t/how-to-bring-the-reference-genome-to-usegalaxy/4999/2 "2020-12-11T17:03:50Z")

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Look at “Custom builds” under the User menu

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### Author: ![agrieng3](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/agrieng3/32/378_2.png) [@agrieng3](https://help.galaxyproject.org/u/agrieng3)
#### Post date: [December 14, 2020, 8:29pm UTC](https://help.galaxyproject.org/t/how-to-bring-the-reference-genome-to-usegalaxy/4999/3 "2020-12-14T20:29:30Z")

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Thanks, can you tell me how i can use this option in usegalaxy?

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### Author: ![innovate-invent](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/innovate-invent/32/734_2.png) [@innovate-invent](https://help.galaxyproject.org/u/innovate-invent)
#### Post date: [December 14, 2020, 8:47pm UTC](https://help.galaxyproject.org/t/how-to-bring-the-reference-genome-to-usegalaxy/4999/4 "2020-12-14T20:47:01Z")

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> **[Custom Genomes](https://galaxyproject.org/learn/custom-genomes/)**

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### Author: ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [March 17, 2026, 6:14am UTC](https://help.galaxyproject.org/t/how-to-bring-the-reference-genome-to-usegalaxy/4999/5 "2026-03-17T06:14:58Z")

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