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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)arrow-up-right app or DRAGEN Reference Builder apparrow-up-right (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.arrow-up-right

Users can also download FASTA file from public databases or from iGenomesarrow-up-right.

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 [email protected]envelope.

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