Dear community,

I am trying to build a pagenome reference graph based only on the two haploid assemblies (chromosome scale) of a diploid species (Vitis vinifera). This graph is meant to be used as a reference to map RNAseq reads of the same species and perform haplotype aware and allele specific expression analysis.

My first doubt is if i should label the described assemblies using the haplotype code (.1) and (.2) or if should label them as two haploid genomes in the SeqFile that is needed by the canctus-pangenome pipeline.

My next doubt is if should use both assemblies as reference or just pick one of them in the --reference flag. I don't have any reasons to pick one over the other quality wise, since they are both the same.

I will appreciate any insights.