# Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at **URL:** \ **Category:** Resources\ **Tags:** fasta-manipulation, custom-genome, reference-genome, custom-build, resources\ **Created:** [May 17, 2023, 9:19pm UTC](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 "2023-05-17T21:19:25Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![Fabiano\_Menegidio](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/fabiano_menegidio/32/1024_2.png) [@Fabiano\_Menegidio](https://help.galaxyproject.org/u/Fabiano_Menegidio)\ **Post date:** [May 17, 2023, 9:19pm UTC](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/10082/1 "2023-05-17T21:19:25Z")
Reference data: no option available Contact the administrator of this Galaxy instance if you miss reference data (–config-dir) ![Screenshot_20230517_182122_Chrome](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/ca4fdd6b31630ddc713406d44e2d6719e1d3fa15.jpeg) ---
**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:** [May 17, 2023, 11:01pm UTC](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 "2023-05-17T23:01:55Z")
Hi @Fabiano_Menegidio **For immediate use** , try using the **custom genome** feature. > **[Galaxy Training: How to use Custom Reference Genomes?](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html)** > > Collection of tutorials developed and maintained by the w... If you need to assign a **database** metadata to datasets, your custom genome can be promoted to a **custom build**. > **[Galaxy Training: Adding a custom database/build (dbkey)](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_add_custom_build.html)** > > Collection of tutorials developed and maintained by the w... * * * * * * **For use later on** , please post back details about the genome and we can consider adding it to the native reference indexes. We’ll need enough information to locate the data, and the genome should be from a public source. Not all genomes can be added but it doesn’t hurt to ask 🙂 ---
**Author:** ![Fabiano\_Menegidio](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/fabiano_menegidio/32/1024_2.png) [@Fabiano\_Menegidio](https://help.galaxyproject.org/u/Fabiano_Menegidio)\ **Post date:** [May 18, 2023, 4:06pm UTC](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/10082/3 "2023-05-18T16:06:04Z")
I had previously created a custom genome for my species (with a mitochondrial genome) and followed both steps. However, these custom genomes are not enabled in the “Reference data” field of Get Organelle from reads. However, Get Organelle does not expect a reference genome as a mandatory parameter, but rather a database from a clade. Can you please validate this for me? ---
**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:** [May 21, 2023, 10:39pm UTC](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/10082/4 "2023-05-21T22:39:43Z")
Hi @Fabiano_Menegidio Ok, thanks for explaining. Please try the tool at [UseGalaxy.eu](http://UseGalaxy.eu) since they have more indexed data specific for this tool. **To be clear to anyone reading:** [Custom genome functions](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html) work with the vast majority of tools – and are for when _a single genome is needed_. This guide explains how it works → [Reference genomes at public Galaxy servers: GRCh38/hg38 example](https://help.galaxyproject.org/docs?topic=11616) ← along with a bit of extra help for human variants, but the same process works for **any fasta file that you want to use as a reference** (genome, transcriptome, exome – all) The few tools that do not compare to a single genome, but a merged index of several genomes or parts of genomes (organelles), are a different comparison analysis concept and do sometimes require a special server-side index. At least one of the public UseGalaxy servers likely hosts what you need – so please check first, then ask and we’ll try to address anything still needed. Be specific: server URL, tool name/version, and the exact reference index you cannot find and cannot use the custom genome functions to resolve. ---
**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:** [January 30, 2024, 5:52pm UTC](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/10082/5 "2024-01-30T17:52:09Z")
Split this topic on January 30, 2024, 5:52pm UTC A post was split to a new topic: [Custom reference genome troubleshooting](https://help.galaxyproject.org/t/custom-reference-genome-troubleshooting/11624) ---
**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:** [January 30, 2024, 6:07pm UTC](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/10082/6 "2024-01-30T18:07:33Z")
Closed on January 30, 2024, 6:07pm UTC