# A built-in reference genome is not available for zebrafish to utilise HISAT2

**URL:** <https://help.galaxyproject.org/t/a-built-in-reference-genome-is-not-available-for-zebrafish-to-utilise-hisat2/17651>\
**Category:** usegalaxy.org support\
**Tags:** custom-genome, custom-build\
**Created:** [April 13, 2026, 1:28pm UTC](https://help.galaxyproject.org/t/a-built-in-reference-genome-is-not-available-for-zebrafish-to-utilise-hisat2/17651 "2026-04-13T13:28:52Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Rahul\_Madaan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/rahul_madaan/32/8582_2.png) [@Rahul\_Madaan](https://help.galaxyproject.org/u/Rahul_Madaan)\
**Post date:** [April 13, 2026, 1:28pm UTC](https://help.galaxyproject.org/t/a-built-in-reference-genome-is-not-available-for-zebrafish-to-utilise-hisat2/17651/1 "2026-04-13T13:28:52Z")

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How do i move ahead…Is there any built in reference genome available that I can just directly upload onto it (from ENSEMBL ?)

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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:** [April 13, 2026, 7:51pm UTC](https://help.galaxyproject.org/t/a-built-in-reference-genome-is-not-available-for-zebrafish-to-utilise-hisat2/17651/2 "2026-04-13T19:51:59Z")

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Hi @Rahul_Madaan

Hopefully we can help!

You can use a **Custom Genome** with any tool. All that is needed is a `fasta` file in your history.

- [Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at - #2 by jennaj](https://help.galaxyproject.org/t/custom-genome-custom-build-how-to-use-a-genome-that-is-not-natively-indexed-at-the-server-you-are-working-at/10082/2)
- Then, see the Mapping step in this tutorial (or try it all, this is our primary introduction and is worth it!) → [Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses](https://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/tutorial.html)

Which `fasta` to choose has considerations.

1. Choose the reference annotation at the same time (`gtf` or `gff3` file). Please be aware that some Bioconductor tools do not parse raw Ensembl identifiers (with version) well, and using a UCSC version that has been sanitized a bit can be easier. Or, you can [remove the `.N` parts of the accession yourself](https://help.galaxyproject.org/t/how-to-replace-these-id-with-official-gene-names/726/5) (from all files!) if an error or odd result comes up.

2. Consider where you plan to visualize your data. IGV is available to all genomes, including custom genomes, [but has a few extra steps to create the database key](https://help.galaxyproject.org/t/bam-index-fasta-indexes-display-applications-custom-genome-builds-igv/16283/4). If you [sourced the data from UCSC instead](https://help.galaxyproject.org/t/rseqc-read-distribution-is-mostly-utr-instead-of-exons-for-mrna-seq/8690/2), and used their version of the genome and annotation (including the Ensembl genes track), and assigned a native database key, then everything would be native in both IGV and and at UCSC.

More help at #custom-genome #custom-build #reference-genome #reference-annotation #igv

Please give this a try a follow-up questions are welcome! 🙂