Creating custom reference genomes (non human) to use with DRAGEN apps on BaseSpace Sequence Hub

DRAGEN requires reference genomes to be converted into a hash table format.

To use a custom reference genome (non-human) with DRAGEN apps in BaseSpace Sequence Hub (BSSH), use the DRAGEN Reference Builder app(consideration depends on which DRAGEN App(s) versions will be used for analysis) to convert a reference genome in FASTA format to a hash table. User is recommended to check the App Description of intended application for the requirement of the custom hash table.

Table listing recommended DRAGEN Reference Builder app version for different major DRAGEN versions

DRAGEN version	Hash table version	DRAGEN Reference Builder app version
4.5	12	4.5.4000
4.4	11	4.4.6002
4.3	10	4.3.6002
4.2	9	4.2.4002
3.5 - 4.1	8	3.7.8802

Once the DRAGEN Reference Builder app has built a custom hash table, use DRAGEN apps with 'Custom' Reference option.

The DRAGEN apps typically provide built-in support for hg19, hg38, CHM13, and hs37d5. The DRAGEN Reference Builder app is meant for users who need to generate a custom, non-human or non-standard reference.

Where to download the FASTA/GTF file?

For custom genomes for RNA analysis, Illumina recommends using GTF files (& genomes) from Ensembl. Additionally mm9, mm39 and rn6 references are available by default for the latest DRAGEN Single Cell RNA and DRAGEN RNA applications.

Users can also download FASTA file from public databases or from iGenomes.

How to upload the fasta/GTF files to BaseSpace?

To upload FASTA/GTF files to BaseSpace Sequence Hub (BSSH): open a project, select the File icon, then select Upload > Files > Misc . Alternatively such files can be uploaded using BaseSpace CLI or API.

The FASTA file extension must be either .fasta or .fa or the apps will not recognize it.The GTF file extension must beeither .gtf or .gtf.gz or the apps will not recognize it.

For any feedback or questions regarding this article (Illumina Knowledge Article #7488), contact Illumina Technical Support [e-mail].