Creating a custom DRAGEN reference genome for NextSeq1000/2000 analysis

Creating a custom DRAGEN reference hash table/genome for NextSeq1000/2000 analysis

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

● On the NextSeq 1000/2000, the pre-loaded genomes are already converted to hash tables.

● To use a custom reference genome for NextSeq1000/2000, use the BSSH Reference Builder (Instruments) app to convert a reference genome in FASTA format to a hash table.

For custom genomes, we recommend using GTF files (& genomes) from Ensembl

To upload FASTQ/GTF files to BaseSpace Sequence Hub (BSSH), open a project, click the File icon, and select Upload > Files > Misc/Others

Reference Builder for Illumina Instruments app input files:

Reference genome in FASTA format - the file must use extension .fasta or .fa.

Gene annotation file in GTF format - the file must be gzipped and must use the extension gtf.gz.

Custom genomes built using the BSSH Reference Builder (Instrument) app are available in the BSSH Run Planning Reference Genome menu under Analysis Setting. After running the BSSH Reference Builder (Instrument) app, the custom genome is ready for use in Cloud analysis.

To use a custom genome for Local analysis, the genome must be imported on-instrument through the NextSeq 1000/2000 Control Software.

The output of the BSSH Reference Builder for Illumina Instruments app is a \*.tar.gz file.

Download the \*.tar.gz file and import it through the NextSeq 1000/2000 Control Software.

Importing a custom genome:

You must be logged in as ilmnadmin to import genomes.

After import, the custom genome is found in the genome repository:

/usr/local/illumina/genomes

For any feedback or questions regarding this article (Illumina Knowledge Article #7055), contact Illumina Technical Support [e-mail].