> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/software/dragen/software-dragen-reference_material-list/000009925.md).

# How to build a Custom Reference Hashtable for BaseSpace DRAGEN Single Cell RNA Application

DRAGEN uses hashtable references to map sequence reads to a reference genome. It generates hashtables from FASTA files, which serve as input. These hashtables are a custom binary format of the reference genome required by DRAGEN. The hashtable version must match the one expected by the DRAGEN Single Cell RNA Analysis pipeline.

Refer to the table below for compatibility:

|                          | Analysis Setup    | Hashtable Version | Hash Table Application                 |
| ------------------------ | ----------------- | ----------------- | -------------------------------------- |
| DRAGEN Single Cell 4.4.2 | Run Planning      | 10                | Reference Builder (Instruments) v3.0.0 |
| DRAGEN Single Cell 4.4.2 | Manual App Launch | 10                | DRAGEN Reference Builder 4.3.6         |
| DRAGEN Single Cell 4.4.4 | Manual App Launch | 11                | DRAGEN Reference Builder 4.4.4001      |

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9925), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009925%20-%20Software%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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