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 checking App Description for the requirement of custom hash table.

Once the DRAGEN reference builder app is done, use DRAGEN apps with Custom Genome option.

The DRAGEN apps typically provide built-in support for hg19, hg38, GRCh37, and hs37d5. The Reference Builder app is meant for users who need to generate a custom, non-human or non-standard reference.

DRAGEN reference builder app is different from Reference Builder (Instruments) app where Reference Builder (Instruments) was used for on-instrument or Run Planning set up analysis with custom genomes.

Where to download the FASTA/GTF file?

For custom genomes for RNA analysis, Illumina recommends using GTF files (& genomes) from Ensembl.

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

The file extension must be .fasta or .fa, or the apps will not recognize it.

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