Calculate ‘R80’ and associated statistics for each performed Stacks run.
optimize_m()
Optimize the m parameter during denovo stacks assembly
optimize_bigM()
Optimize the M parameter during denovo stacks assembly
optimize_n()
Optimize the n parameter during denovo stacks assembly
Use the stats from your Stacks runs to determine optimal parameter settings.
vis_depth()
Visualize the effect of varying the m parameter on the mean depth of each sample
vis_snps()
Visualize the effect of varying a stacks parameter on the number of SNPs retained
vis_loci()
Visualize the effect of varying a stacks parameter on the number of polymorphic loci retained