Comments (2)
Hi,
By default Panaroo removes rare edges that connect more conserved gene clusters. This helps to make the graph easier to view by reducing the impact of assembly errors.
As you have high quality genomes you can turn this off using the --no_clean_edges
flag.
Please let me know if this does not fix the issue.
from panaroo.
Thanks for the explanation!
Changing that flag resulted in the nodes being incorporated into the rest of the network.
from panaroo.
Related Issues (20)
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from panaroo.