Using Mate Pair Information in de Bruijn Graphs

This is our last post in the de Bruijn graph series. Although we did not mention explicitly, each of the previous posts was written to present a conceptual building block for the operations of de Bruijn graph-based assemblers. Only thing we did not discuss yet is how the assembly is really done.

For argument’s sake, imagine you are sequencing a very short gene using the shotgun approach. The sequencer gave you fragments for various parts of the gene, and you have to stitch them together to reconstruct the entire gene.

For a small gene, the stitching together is usually done by aligning all reads and taking the consensus sequence. Sequencing errors are expected to be removed by the consensus generating process.

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