Extract node information from de Bruijn graph

[holmrenser]

I want to extract some specific properties of the nodes of the de Bruijn graph, following the methods of this publication: Wetzel et al.: Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics 2011 12:95.

I have been using SOAPdenovo to create assemblies, which is a de Bruijn graph based assembler. I am however struggling with extracting the de Bruijn graph information from the SOAP output.

What I want to know is the number of incoming/outgoing edges of each node to assess repeat structure of the genome.

Any thoughts?

Sincerely,

Rens Holmer

EDIT: Just use velvet to construct the graph. Solved.