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Old 07-17-2013, 07:35 AM   #1
holmrenser
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Location: Netherlands

Join Date: Jul 2013
Posts: 9
Default Extract node information from de Bruijn graph

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.

Last edited by holmrenser; 07-18-2013 at 01:01 AM.
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