# FAQ: NCBI reference data

**URL:** <https://help.galaxyproject.org/t/faq-ncbi-reference-data/15720>\
**Category:** Resources\
**Tags:** reference-index, reference-annotation, reference-genome, resources\
**Created:** [June 12, 2025, 8:36pm UTC](https://help.galaxyproject.org/t/faq-ncbi-reference-data/15720 "2025-06-12T20:36:23Z")\
**Posts on this page:** 2\
**Page:** 1

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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:** [June 12, 2025, 8:36pm UTC](https://help.galaxyproject.org/t/faq-ncbi-reference-data/15720/1 "2025-06-12T20:36:23Z")

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### 💬 How to find NCBI Reference data?

**Q: Where can I find the URL links to a reference genome FASTA, annotation, or GenBank file?**

**A:** Use the **NCBI Genome Assembly page** for the organism of interest — for example:  
[https://www.ncbi.nlm.nih.gov/datasets/genome/GCF\_000819615.1/](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000819615.1/)

This page provides:

- Download links for genome sequences (FASTA)
- Annotation files (GFF, GTF)
- GenBank format files _(used with SnpEff build)_
- Direct links to the associated FTP directories

Screenshot of a NCBI genome assembly view for [GCF\_000819615.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000819615.1/)

 ![ncbi-assembly-details-1](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/3/360505119078733b4878a51325e1a5f94659e02a.png)

Screenshot of a NCBI genome **FTP** directory view for [GCF\_000819615.1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000819615.1/)

 ![ncbi-assembly-details-2](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/6/676622b801d94b976477b9b4ff0d4d87d9296875.png)

| File name | Description |
| --- | --- |
| `genomic.gbff.gz` | Reference **GenBank** record (for SnpEff build) |
| `genomic.gtf.gz` | Reference **gene annotation** (GTF format) |
| `genomic.fna.gz` | Reference **genome FASTA** sequence |

### 🔗 How to get the data into Galaxy?

1. Capture the URL link for your file(s)
2. Paste into the ⬆ **Upload** tool
3. Click on **Start** using all default settings
4. The files will be loaded into your current **Active** history

### 🛠 Standardizing the format

1. With some tools, getting the data loaded is enough!
2. With others, you may want to remove the description content from the FASTA `>` lines and/or remove the `#` header lines from the GTF.

### 🧑‍🔬 How to use the data with tools or a workflow?

1. Use the input option to **Choose Reference Data from the History**
2. Select your dataset file.
3. If the data requires a tool index (example: mapping tools), the index will be automatically created at runtime.
4. If you need a **custom database** key for visualization options, you can create and assign one!

### 📘 Resources

- [Getting Data into Galaxy](https://help.galaxyproject.org/t/getting-data-into-galaxy/10868)
- [FAQ: How to use Custom Reference Genomes?](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html)
- [FAQ: Working with GFF GFT GTF2 GFF3 reference annotation](https://training.galaxyproject.org/training-material/faqs/galaxy/datasets_working_with_reference_annotation.html)
- [FAQ: Extended Help for Differential Expression Analysis Tools](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_differential_expression_help.html)
- [FAQ: Adding a custom database/build (dbkey)](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_add_custom_build.html)
- **Assembly Version?** See → [Reference genomes at public Galaxy servers: GRCh38/hg38 example](https://help.galaxyproject.org/t/reference-genomes-at-public-galaxy-servers-grch38-hg38-example/11616)

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<div class="post-metadata">

**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:** [August 13, 2026, 9:06pm UTC](https://help.galaxyproject.org/t/faq-ncbi-reference-data/15720/3 "2026-08-13T21:06:46Z")

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