I’ve been looking for a program that allows me to visualize pangenomes efficiently and it has been very difficult find satisfactory documentation about large pangenome’s visualization tools since most of them are related to prokaryotic genomes (which are smaller size) and/or chunks of eukaryotic genomes to study specific haplotypes.
My pangenome has these characteristics:
nodes 18424540
edges 24616683
length 1069101379
My objective is to be able to get an image of the full pangenome or one for each chromosome, from which has to be possible to interpret approximatevly its structure and where significant divergence between the genome sequences is found.
So far the programs I have been using were not able to give a meaningful image of the eukaryotic pangenome in question.
I come here to ask if anyone has found him/herself in this situation before, and if you manage to find a solution or even a compromise to still be able to have an idea of its structure indirectly, it would be very much of help for me!
Thank you in advance
My pangenome has been created following the Cactus pipeline step-by-step (skipping the optional 3rd step).
Tags should also include [pangenome] and [minigraph-cactus]
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