I'm wondering what would be the best strategy to obtain the list of all k-mers in the graph with each k-mer labeled as reference (i.e., from specific path) or not-reference. A very nice to have extra feature would be to have, for each k-mer, the index(es) of its occurrence(s) in the reference (linear) space.
I see two possible roads:
vg kmers ... vg find -k ...
Both strategies have prons and cons. The former produces more succinct output but I haven't found a way to discriminate whether k-mers belongs or not to a path (nor I found an easy way to obtain the index). The latter has more extensive output, but also produces much larger outputs.
Thanks for any suggestion, Michele S.