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Question: How to handle Reverse complement in De-Bruijn Graph
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gravatar for kshitijtayal
3.4 years ago by
kshitijtayal • 30
India
kshitijtayal • 30 wrote:

I am trying to do denovo assembly using De Bruijn Graph. What are the different ways by which i can  handle/consider reverse complements reads while constructing de Bruijn graph 
next-gen assembly genome • 1.6k views
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modified 3.4 years ago by Rob ♦ 3.2k • written 3.4 years ago by kshitijtayal • 30
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gravatar for Rob
3.4 years ago by
Rob ♦ 3.2k
United States
Rob ♦ 3.2k wrote:

The standard methodology is to associate a single de Bruijn graph node with both a k-mer and its reverse complement.  If you take a look at e.g. GATB's excellent implementation, you'll see that this is how they handle it.  The problem is that when processing sequencing reads, you really have no idea what strand a read was drawn from, and so you don't really have a good way to distinguish between the two.  It's also worth noting that one typically builds de Bruijn graphs with only odd-sized k-mers.  This prevents the scenario where a k-mer is its own reverse-complement.  
ADD COMMENT • link written 3.4 years ago by Rob ♦ 3.2k

Many thanks for the prompt reply. After reading your reply , one more question arises in mind that if every graph node has two values then which value to take in case of Eulerian walk ? I was wondering if there are any existing tools for viewing a de Bruijn graph from raw reads?

ADD REPLY • link modified 3.4 years ago • written 3.4 years ago by kshitijtayal • 30
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