Tiling algorithm
The tiling algorithm selects a subset (a tiling) of the input amplicons that meets the following criteria.
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Covers as much of each target sequence as does the original input.
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Has many fewer amplicons than the input set.
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Maximizes the quality of the amplicons.
To do this, the tiling algorithm performs the following steps.
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Creates an overlap graph of candidate inserts.
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Assigns a cost to each edge.
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Returns the tiles from the least-cost path from source to sink.
The output from the tiling algorithm is used as input for the pooling algorithm.
Improvements in the tiling algorithm have significantly increased the in silico coverage of the designs. The users are enabled to choose between in silico and assay performance.