- 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 asmflag and augment the corresponding haplotype paths asWlines 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
Wlines. - Script Gen_Graph.py can be used/modified to generate pangenome graphs from Human C4 sequences stored in Genomes folder.
test
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