Import Resource Files

You can import reference genomes or reference files. For a list of on-instrument reference genomes, refer to the NovaSeq X Series Product Compatibility page. You can remove existing reference genomes or reference files to clear hard drive space.

You can add and delete reference genomes on the Genomes tab in the Resources settings screen. The Genomes tab displays the genome name, if they are a standard or custom genome, the species, and the genome source.

1. Make sure that there are no sequencing runs or on-instrument secondary analyses in progress.
2. Select the instrument icon to open the global navigation menu.
3. Select Settings, and then select Resources.
4. On the Genomes tab, select Import Genome.
5. Navigate to the reference genome (*.tar.gz), and then select Open.
6. Select Import.

Import Reference Files

You can add and delete reference files on the Reference Files tab in the Resources settings screen. The Reference Files tab displays the reference file name, file type, file description, and the number of related reference genomes.

If performing CNV calling, you can use an optional panel of normals file. The panel of normals file is a reference based normalization algorithm that uses externally supplied matched normal samples to determine a baseline level from which to call CNV events. These matched normal samples should be derived from the same sample type, library prep, sequencing workflow that is used for the case sample. The algorithm subtracts system level biases that are not sample specific.

You can use a panel of normals file for both somatic and germline variants.

If using the DRAGEN Enrichment secondary analysis, you can use a noise baseline file to filter out sequencing or systematic noise. You can download standard custom noise files from the Illumina Support Site or create a custom noise baseline file.

Use one of the following options to generate a panel of normals or noise baseline file. It is recommended to use ~50 samples.

• Use the DRAGEN server. Refer to the Illumina DRAGEN Bio-IT Platform support site page for instructions.
• Use DRAGEN Baseline Builder App on Illumina DRAGEN Bio-IT Platform, which accepts FASTQ, BAM, or CRAM. The Baseline Builder App generates a CNV Baseline file (*.combined.counts.txt.gz file).
1. Make sure that there are no sequencing runs or on-instrument secondary analyses in progress.
2. Select the instrument icon to open the global navigation menu.
3. Select Settings, and then select Resources.
4. On the Reference Files tab, select Import reference file.
5. Navigate to the reference file, and then select Open.
6. [Optional] Enter a description for the reference file.
7. Select a file type from the drop-down list.

If your file type is not listed, select Other and enter the file type in the field that appears.

8. Select the reference genomes related to the reference file.
9. Select Save.