# Sus Scrofa 11.1 reference genome in Freebayes

**URL:** <https://help.galaxyproject.org/t/sus-scrofa-11-1-reference-genome-in-freebayes/10342>\
**Category:** usegalaxy.eu support\
**Tags:** devops-administration, freebayes, mapping, reference-genome\
**Created:** [June 26, 2023, 5:41pm UTC](https://help.galaxyproject.org/t/sus-scrofa-11-1-reference-genome-in-freebayes/10342 "2023-06-26T17:41:49Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![lee1](https://avatars.discourse-cdn.com/v4/letter/l/f9ae1b/32.png) [@lee1](https://help.galaxyproject.org/u/lee1)\
**Post date:** [June 26, 2023, 5:41pm UTC](https://help.galaxyproject.org/t/sus-scrofa-11-1-reference-genome-in-freebayes/10342/1 "2023-06-26T17:41:49Z")

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Hi, I performed HISAT2 using the in-built Pig Feb.2017 (Sscrofa11.1/susScr11) susScr11) reference genome. The same genome is not available in the Freebayes tool. If I upload a reference genome (SusScr11.1) from history, will there be an issue due to different versions of the genomes for HISAT2 and Freebayes? If so, can the admin team please add the Pig Feb.2017 (Sscrofa11.1/susScr11) susScr11) reference genome to Freebayes?

Thank you for your assistance.

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**Author:** ![igor](https://avatars.discourse-cdn.com/v4/letter/i/dec6dc/32.png) [@igor](https://help.galaxyproject.org/u/igor)\
**Post date:** [June 27, 2023, 8:48am UTC](https://help.galaxyproject.org/t/sus-scrofa-11-1-reference-genome-in-freebayes/10342/2 "2023-06-27T08:48:35Z")

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Hi @lee1  
if you use the same genome version, the tool should work. Maybe try susScr11 from UCSC Genome Browser (download section). It does not take a lot of time.  
Kind regards,  
Igor