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
Question: How to handle Reverse complement in De-Bruijn Graph
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kshitijtayal • 40 wrote:
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modified 5.3 years ago
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Rob ♦ 4.6k
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5.3 years ago by
kshitijtayal • 40
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Rob ♦ 4.6k 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.
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