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human-pangenomics / hpp_pangenome_resources

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genome graph generated by Minigraph #21

Open yihangs opened 9 months ago

yihangs commented 9 months ago

The document says that the graph generated by Minigraph has no cyclic, which from my understanding, is a directed acyclic graph. However, when I checked the file hprc-v1.0-minigraph-grch38.gfa, I find that there are edges from one + node to a - node (e..g L s424632 + s757 -), so it does not look like a DAG to me. Can you help explain on that?

Thanks!

glennhickey commented 9 months ago

By having no "cyclic paths", the document means there are no labelled paths in the graph that are cyclic. The graph itself contains reversing edges and is therefore, like you point out, cyclic.

yihangs commented 9 months ago

Thanks! Do these graphs contain inter-chromosomal edges? Or they are actually a sum of distinct graphs, each representing one chromosome?

glennhickey commented 9 months ago

One component / chromosome (including unplaced contigs for grch38-based graphs)