Overview of the genotype aware alignment workflow.

Sequence gene content, determined by PING copy, informs the selection of reference sequence from a predefined set of diverse allele sequences. An exhaustive alignment is performed to the selected allele set, from which an initial genotype determination is made. The determined genotype informs selection of reference alleles for a genotype aware alignment, followed by another round of genotype determination. The genotype aware alignment and subsequent genotype determination is repeated, and the most congruent genotypings across all alignment rounds inform reference selection for a final round of alignment. A non-exhaustive alignment is performed to the selected allele set, from which all aligned reads are processed and used for the final genotype determination.