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 BaseSpace Reference Builder (Instruments) app or DRAGEN Reference Builder app (depending on which DRAGEN App(s) will be used for analysis) to convert a reference genome in FASTA format to a hash table.

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

DRAGEN apps that require the DRAGEN Reference Builder app to generate custom genomes:

• DRAGEN RNA Pipeline

• DRAGEN Germline

• DRAGEN Somatic

• DRAGEN Enrichment

The output file from DRAGEN Reference Builder is a .v8.tar file which contains the DRAGEN Reference.

DRAGEN apps that require the BSSH Reference Builder (Instruments) app to generate custom genomes:

• DRAGEN RNA 3.8.4+

• DRAGEN Amplicon

• DRAGEN Single Cell RNA

• DRAGEN Single Cell ATAC

• DRAGEN Imputation

Reference Builder (Instruments) App includes the following features:

• Support NextSeq 1000/2000

• Support DNA analysis with CNV calling

• Support RNA analysis

• Support building alt-aware reference genomes with custom liftover files as well as built-in hg19 and hg38 liftover files

• Support optional default GTF annotation file (gzipped) for RNA analyses

The output file from Reference Builder (Instruments) App is a gzipped TAR file which contains the DRAGEN Reference.

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 FASTQ/GTF files to BaseSpace Sequence Hub (BSSH): open a project, select the File icon, then select Upload > Files > Misc/Others.

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 [e-mail].