How can you connect the ends of these contigs? One idea is to make primers to each of the 2 x 200 contigs and, using every pairwise combination, try to amplify DNA from S. sanguis. Only those pairs that are close to each other on the genome should yield PCR products. This is a great idea. Unfortunately, it requires doing approximately 160,000 PCR reactions, more than you have patience for.

You need a trick to reduce the number of PCR reactions to a manageable number. What would take years for physical tubes and enzymes is the work of a moment for virtual PCR. Your thoughts turn to ways to simulate PCR, producing candidate pairs of contigs, which could be confirmed by real PCR.

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