Before a reference genome can be used with DRAGEN, it must be converted from FASTA format into a custom binary format for use with the DRAGEN hardware. The options used in this preprocessing step offer tradeoffs between performance and mapping quality.
The DRAGEN system is shipped with reference genomes hg19 and GRCh37. Both reference genomes are preinstalled based on recommended settings for general applications. If you find that performance and mapping quality are adequate, there is a good chance that you can simply work with these supplied reference genomes. Depending on your read lengths and other particular aspects of your application, you may be able to improve mapping quality and/or performance by tuning the reference preprocessing options.