Fig. 2: Alignments of the two main haplotigs to the primary GRCh37 MHC region.
From: A diploid assembly-based benchmark for variants in the major histocompatibility complex
We compute the local divergence (est. difference) of the HG002 MHC haplotigs to the MHC of GRCh37 by performing local alignment. The differences between the assembled contigs to the references are computed using sequence blocks anchored with minimers and aligned locally using an O(ND) alignment algorithm33.
