Sequence divergence of input genomes

[majunyeong]

I wonder if it is possible to use a genome set with up to 5% sequence divergence as an input for panGraph.

[mmolari]

Hi @majunyeong,
Currently 5% sequence divergence is on the upper limit of what panGraph can handle. We're working to remove this limitation, but in the current version I expect that some of the matches for the most diverged parts of the sequence might be missed.
In the meantime you can try to run pangraph build with the --sensitivity 20 option, which under the hood calls the minimap2 aligner with -x ams20 option. This improves the quality of matches for more diverged sequences.
Hope this helps!