DiGi Datasets

This dataset contains the MHC assemblies used in our paper: 108 haplotypes from 54 HGSVC3 samples, 10 test haplotypes from 5 samples (HG002, I002C, HG005, HG01106, HG02055), and the GRCh38 MHC sequence (chr6:28,510,125–33,480,577). MHC regions were extracted by aligning each assembly to GRCh38 (no-alt analysis set: GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta) with minigraph. From the 130 HGSVC3 assemblies, we excluded HG002 (a test sample) and both haplotypes of any sample with a contig break in the MHC.

Dataset contents:

1. graph_108_haps.tar.gz: 108 HGSVC3 MHC haplotype assemblies and supporting files used to construct the graph
2. graph_18_haps.tar.gz: 18-haplotype subset of (1)
3. test_and_reference.tar.gz: 10 test haplotypes (HG002 Q100, HPRC year 2 and I002C) and the GRCh38 MHC sequence, none of which are included in (1) or (2).