Abigail Shockey's repositories
MjolnirTree
Construct a neighbor-joining tree using a hamming distances calculated from a gene presence/absence matrix
docker-builds
Dockerfiles and documentation on tools for public health bioinformatics
dryad
Generate various phylogenetic trees from raw short read sequences
genomeClusterReport
Generate a genomic clustering report using R Markdown
ggtree
:christmas_tree:Visualization and annotation of phylogenetic trees
midwest-region
Site for AMD Midwest Region
snp-pipeline
SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
spriggan
Spriggan is a pipeline used for assembly of bacterial whole genome sequence data and identification of antibiotic resistance genes.
staphb_toolkit
Python Toolkit for using containerized programs in either Singularity or Docker
trees
Scripts for generating and plotting trees
webinar_materials
Repository for the scripts and other materials from webinars I've developed