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Question: How to handle Reverse complement in De-Bruijn Graph
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gravatar for kshitijtayal
4.8 years ago by
kshitijtayal • 40
India
kshitijtayal • 40 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 • 2.1k views
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modified 4.8 years ago by Rob ♦ 4.0k • written 4.8 years ago by kshitijtayal • 40
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gravatar for Rob
4.8 years ago by
Rob ♦ 4.0k
United States
Rob ♦ 4.0k 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 modified 8 months ago by RamRS ♦ 28k • written 4.8 years ago by Rob ♦ 4.0k

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 4.8 years ago • written 4.8 years ago by kshitijtayal • 40
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