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Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data

Figure 1

Modules of HighMap algorithm.

A: The single-linkage clustering algorithm was used to partition the marker loci into linkage groups based on a pairwise modified independence LOD score for the recombination frequency. B and B': The ordering module combines Gibbs sampling, spatial sampling, and simulated annealing algorithm to order markers and estimate map distances. C: The error correction module identified singletons according to parental contribution of genotypes and eliminated them from the data using k-nearest neighbor algorithm. To order markers correctly, the processes of ordering and error correction were carried out iteratively. D: Heat maps and haplotype maps were constructed to evaluate map quality.

Figure 1

doi: https://doi.org/10.1371/journal.pone.0098855.g001