Best way to obtain reference and non-reference k-mer

Question

[michele.schimd]

Hi everyone,

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.

Answer 1

[Jouni Sirén]

The easiest way is probably doing it outside vg:

1. Extract all kmers (kmer occurrences) with vg kmers.
2. Extract the selected paths in FASTA format with vg paths -v graph.vg -F -p path-names.txt > output.fa.
3. Determine the kmers in the paths using an external tool.
4. Compare the kmer sets with an external tool.

The path positions for non-path kmers are not always well-defined. There is some machinery for determining them (for alignments, not kmers), but even then, we often have to make arbitrary choices or give up trying.

[michele.schimd]

Thank you very much for the prompt and detailed reply. I was considering using external tools, but I wanted to be sure that there were no better ways built in the toolkit.