Question: How to handle Reverse complement in De-Bruijn Graph
2
gravatar for kshitijtayal
2.3 years ago by
kshitijtayal30
India
kshitijtayal30 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 • 1.0k views
ADD COMMENTlink modified 2.3 years ago by Rob2.2k • written 2.3 years ago by kshitijtayal30
5
gravatar for Rob
2.3 years ago by
Rob2.2k
United States
Rob2.2k 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 COMMENTlink written 2.3 years ago by Rob2.2k

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 REPLYlink modified 2.3 years ago • written 2.3 years ago by kshitijtayal30
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