code

Standalone programs for data analysis and/or visualization

Mutational Distance from Modal Haplotype Calculator


Interactive shiny app that calculates the modal haplotype from Y chromosomal haplotype data and plots the mutational distance of each individual from that modal haplotype.

Bubble Tree


DOI conda link Bubble tree takes frequency table where taxa are rows and samples are columns, a phylogenetic tree, and a sample metadata file to create either a bubble tree or heatmap with abundances plotted on a phylogenetic tree.

GC content by read length plots


DOI Script calculates summary statistics for read length and GC content from a fastq or fasta formatted file and generates a statistics table and plot. Originally written for Mann et al. 2018

Flag PCR and Optical Duplicates


DOI Script calculates the number of predicted PCR and optical duplicates in a sam file. Returns multiple output files: non-duplicates, PCR duplicates, optical duplicates, and count table (crosstabulation of optical duplicate record groups per sample). Optionally draws figure of location where predicted optical duplicates fall on the tile.