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Generating haplotype-aware pangenome graphs from Human C4 Sequences

Graph Generation

  • To reproduce the results, we begin by downloading 96 Human C4 sequences from the Human Pangenome Reference Consortium (HPRC), which are hosted at Zenodo.
  • We utilize the C4 sequence from the CHM13 cell line as the reference and exclude the GRCh38 cell line C4 sequence.
  • For the remaining 94 sequence, we generate a pangenome graph by augmenting structural variations (SVs) of at least 50 base pairs (bp) with Minigraph.
  • Subsequently, we align each sequence back to the C4 pangenome graph with Minichain using -cx asm flag and augment the corresponding haplotype paths as W lines in the graph.
  • Graphs are generated in Graphs folder, C4-CHM13_mg.gfa is rGFA pangenome graph while C4-CHM13.gfa is GFA v1.1 pangenome graph with W lines.
  • Script Gen_Graph.py can be used/modified to generate pangenome graphs from Human C4 sequences stored in Genomes folder.