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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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GFA file with large amount of nodes & edges #1321

Open SwenDiepstraten opened 6 months ago

SwenDiepstraten commented 6 months ago

Hello,

I have created a pangenome of the subset of my (mammalian) data with minigraph-cactus, but I have a larger amount of edges and nodes than I would expect. I have 1,743,464 nodes and 2,386,085 edges, while only using 1 chromosome of 18 and 5 haplotypes. This makes it difficult to visualize the pangenome. Do you know of any things that can be done?

glennhickey commented 6 months ago

Out of curiosity, how did you calculate the number of nodes and edges that you expect?

SwenDiepstraten commented 6 months ago

I compared with articles, where i seemed to be high in comparison