qianxuans/CHOP-NICU-Scripts: v1.0.0 - CHOP NICU S. aureus Transmission Analysis Scripts

Description Analysis scripts and workflows for the study: "Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection" Contents This release contains custom code used for the analyses described in the manuscript. Limited input and output files are included. Certain data are excluded to protect patient privacy. Genome assembly and quality control Determination of clonality Clonality determination Multi-SNP-threshold plot generation Ready-to-use pipeline available at: https://github.com/microbialARC/THRESHER Cluster analysis and visualizations Swimmer plot Cluster floorplan Cluster plot Spatial distance rescaled phylogenetic analysis Transmission cluster source analysis Transmission cluster source plot Hidden Markov Model analysis and visualization Associated Resources THRESHER pipeline: https://github.com/microbialARC/THRESHER Sequence data: NCBI BioProjects PRJNA1218714, PRJNA1390285, PRJNA1219099 Citation If you use this code, please cite the associated publication.