Tools for finding a walk in a De Bruijn graph

Question

[Roman]

Hi everyone, I'm searching for a tool that can find walks in a De Bruijn graph.

This can be a tool that reads an existing graph from a GFA file (or some other format), or a library.

I am also interested in programs that solve this problem internally, so I can replicate it myself from the code.

Thanks!

[natasha.sernova]

Roman, you can start by yourself. There is a lot of information here about the graphs. See the link below for many related posts. https://www.biostars.org/post/search/?query=de+Bruijn+graph

Answer 1

[Matthias Zepper]

Dodgr is a quite cool C++ software (with R bindings) that can efficiently calculate of many-to-many pairwise distances on Dual-Weighted Directed Graphs. Its main application is in traffic routing, but I have found it quite helpful for teaching the basics of network analysis also in a biological context, e.g. gene regulatory pathways. See the source code and the vignettes.