Introduction | Summary of available functions | Considerations for genome biology | Estimating genotype probabilities in a mapping population | Data import example with UNEAK | Quality control and genotype calling | Examining the output | Results cleanup and export | Estimating genotype probabilities in a diversity panel | Data import example with VCF | Quality control and parameter estimation | Genotype calling | Examining inheritance mode | Other genotype calling functions | $H_{ind}/H_E$ for filtering markers and individuals | Considerations for RAM and processing time | Citing polyRAD

When and why to use this pipeline | Pipeline overview | TASSEL-GBSv2 | If TASSEL-GBS won't work for your dataset | Alignment with Bowtie2 | Grouping tags by alignment sets | Filtering samples and estimating inbreeding | Sorting tags into isoloci and filtering isoloci | Genotype calling

Introduction | Filtering | Samples | Markers | Genotype calling | Analyses with adegenet | Discriminant analysis of principal components (DAPC) | Spatial principal coordinates analysis (sPCA) | Mantel test | Export of genotypes to adegenet | Visualization with UMAP | Analysis of molecular variance (AMOVA) using pegas | Differentiation statistics using polysat | Export to Structure | Did I miss anything?

Introduction | Obtaining and installing polysat | Workflow overview | Getting Started: A Tutorial | How data are stored in polysat | Functions for autopolyploid data | Functions for allopolyploid data | Treating microsatellite alleles as dominant markers | How to cite polysat

Introduction | Data hygiene | The polysat algorithm for allele assignment | The Catalán method of allele assignment | Testing assignment accuracy using simulated datasets