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Mapping assemblies to pangenome graph #110

@Buuxx

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@Buuxx

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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