HLAssign can analyse NGS data generated using the following Kits
Illumina HLA v2 Sequencing Panel
HLAssign can analyse NGS data from randomly fragmented DNA libraries.
Usually a bait based enrichment is performed on this kind of library or a random fragmentation is performed on PCR amplicons.
If you have very deep coverage, it may be possible to analyze whole genome or whole exome data. But AUC (see result data view) should at least be greater than 0.5 (which is rarely the case) and an experienced HLAssign user should validate the results.