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polysat: tools for polyploid microsatellite analysis

polysat is an R package for performing a variety of tasks with microsatellite (SSR) data from polyploid organisms. These include calculation of inter-individual genetic distances, estimation of allele frequencies, conversion between software formats, and assigning alleles to isoloci.

polyRAD: genotype calling with uncertainty from sequencing data in polyploids

polyRAD is an R package that uses read depth from GBS or RAD sequencing experiments to estimate posterior probabilities of genotypes in polyploid and diploid organisms. It can export numerical genotypes as continuous variables weighted across genotype probabilities, improving the accuracy of genome-wide association and other analysis.

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data

TagDigger is written in Python 3 but can be used without any prior programming experience. It reads FASTQ files from genotyping-by-sequencing studies and exports a table of read counts for any user-specified set of barcodes and tags. TagDigger also includes tools for consolidating marker names and tag sequences across multiple projects, and for splitting one FASTQ file into multiple FASTQ files by barcode. A slideshow is available with more information about TagDigger.

R functions for converting SNP data between UNEAK, adegenet, and Structure formats

R function for plotting USDA plant hardiness zones

R function for drawing an arc on a plot by clicking

Grants Received

"Improved modeling of marker-trait associations in polypoid and diploid organisms using genotyping-by-sequencing with genotype uncertainty" US NSF-Advances in Biological Informatics, award number 1661490, 2017-2020, $669,458.