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Hi, I'm trying to map the assemblies from HPRC to their reference pangenome graph (the version 1 minigraph). Each assembly has around 258 contigs. Below is the command I use
GraphAligner -g hprc-v1.0-minigraph-grch38.gfa -f HG00438.maternal.f1_assembly_v2_genbank.fa.gz -a HG00438.maternal.f1_assembly_v2_genbank_aln.gaf -x vg
It seems like it's taking a tremendous amount of time, so I wanted to ask if it's possible to map assemblies with GraphAligner, and what parameter do you recommend using in this case?
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