The well-definedness rests on the two lemmas above, which also tell us that the maps and, mapping parameters to solutions of optimization problems, that are considered in the algorithm are point-to-point.
We used stringent mapping parameters to minimize erroneous base calling and misaligned reads.
We adjusted read mapping parameters to accommodate the expected divergence between H. vulgare lines (∼1%) and between H. vulgare and H. bulbosum (∼3%) (Morrell et al. 2014).
As more data become available from additional crosses and marker analysis, we should be able to better optimize mapping parameters to more accurately reflect genetic distances for our system.
Finally, we optimized the SSAHA sequence mapping parameters to be used as the default finding that for sequences from splinkerette-PCR reactions containing genomic junction fragments of on average 200 bp in length the optimal SSAHA score is 35.
It follows that it is unlikely that the nuclear divergence estimate provided above was underestimated, given that the mitochondrial divergence was found to be 2- to 3-fold higher, suggesting the ability of our mapping parameters to identify most divergent reads.
