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A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
Collection of planning documents, visualizations, and presentations for my dissertation research. "Investigating Multidrug Resistance in Escherichia coli with Phylogenetics and Machine Learning"
AMRFinderPlus-Matrix contains script for processing the output files of AMRFinderPlus and generating a binary matrix that shows the presence or absence of antibiotic resistance genes, stress response genes, and virulence genes in each sample.
PRAWNS: A fast and scalable bioinformatics tool that generates an efficient pan-genome representation of closely related whole genomes to provide a concise list of genomic features