Due to the low coverage and large data size, the Explore edition of the software is strongly suggested for non-targeted datasets. A usual workflow for big data analysis should include Filtering as a starting step. The resulting small read files only contain reads that map to any of the alleles in the IMGT/HLA database and can be analysed and re-analysed significantly faster than the original, unfiltered read files. For HLA genotyping of whole genome or whole exome data, the following settings should be used: all loci has to be selected as targeted in the Configure HLA targeted genes wizard, all reads should be processed and quality based subsampling should be turned off (the latter two parameters can be set in the Advanced HLA Typing wizard).