Question about GFA format

[medvedevgroup]

Question about GFA format

[iminkin]

@rob-p I was afraid the odd/even issue was going to pop-up. I will think about it and try to make a fix soon.

[iminkin]

Hi @rob-p ,

I understand you confusion. The issue is that initially we adopted the edge-centric definition of the graph, i.e. sequences are spelled by edges, with nodes of size $k$ and edges of size $k + 1$. It is due to historical reasons and having a specific application in mind. But in GFA sequences are spelled by nodes, and edges merely indicate overlap. To output GFA, TwoPaCo turns compacted edges of the graph into nodes (segments in GFA terminology), hence they are of size at least $k + 1$ and overlap is $k$. So if you intend to get a node-centric graph with length of nodes $k$, run TwoPaCo with $k - 1$ if it is possible.

Again, sorry for the confusion, I am aware that it pops up all the time (https://www.biostars.org/p/175058/). I have plans to improve documentation to clear things out (I even put it in for 0.9.3: https://github.com/medvedevgroup/TwoPaCo/blob/master/NEWS.md). I just didn't expect people to start using TwoPaCo right away :)

[rob-p]

Hi @IlyaMinkin,

Yup, I understand the confusion here as well. We have often gone back and forth between preferring the node and edge-centric view of the dBG.

I guess my concern with the proposed temporary solution (running with $k-1$) is that we want nodes to have an odd size, so that $k-1$ will always be even. For example, we want nodes of size $k=31$, so I'd have to run TwoPaCo with $k=30$. According to the documentation, $k$ must be odd. Is this, in fact, the case?

Thanks for the quick responses!
Rob