abigailshockey Goto Github PK

artic_ncov19_ont_nextflow

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

github_tutorial

midwest-region

Site for AMD Midwest Region

mjolnirtree

Construct a neighbor-joining tree using a hamming distances calculated from a gene presence/absence matrix

portfolio

reports

A repository for genomic analysis reports

scripts

Collections of miscellaneous scripts

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.

sputum

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