I am trying to use vg giraffe to map short reads against my pan-genome graph of a genus of Grasshoppers (created from 30 different mitochondrial genomes). The graph is not the most conserved because the divergence between different sequences is quite high (at least compared to humans).
My problem is that I am mapping very few reads with giraffe. I am assuming that my parameter settings are off (I am using the default atm), but I am unsure of how to adjust them to fit my graph. My minimizer file is set with a k = 20 and a w=10.
Do you have any suggestions?
Thank you in advance for your help! -Nicola