Optimize the De Novo Stacks Pipeline via R
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Documentation for package ‘RADstackshelpR’ version 0.1.0
Help Pages
| optimize_bigM | Optimize the M parameter during denovo stacks assembly |
| optimize_m | Optimize the m parameter during denovo stacks assembly |
| optimize_n | Optimize the n parameter during denovo stacks assembly |
| vis_depth | Visualize the effect of varying the m parameter on the mean depth of each sample |
| vis_loci | Visualize the effect of varying a stacks parameter on the number of polymorphic loci retained |
| vis_snps | Visualize the effect of varying a stacks parameter on the number of SNPs retained |