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?
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
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?