Resistant_STEC_MI

Shiga Toxin-Producing Escherichia coli (STEC) Bioinformatic Analysis - Michigan Department of Health and Human Services (MDHHS) and Manning Lab Collaboration

Description:

This repository contains the scripts used for bioinformatics and gene extractions associated with Mukherjee et al., 2021 publication in Antimicrobial Agents and Chemotherapy. Dr. Sanjana Mukherjee, Ph.D., M.Sc., led this work, a collaboration between the MDHHS and the Manning Lab at Michigan State University.

Data Availability:

Sequences are available at BioProjects PRJNA596289, PRJNA514245, PRJNA218110 and PRJNA368991.

Key Features:

• Raw Data Management
• Genome Assembly and Annotation
• Comparative Genomics
• Antibiotic Resistance
• Gene extraction

Bioinformatics Drawing:

Please see the incredibly artistic flow chart below! Wow! This flowchart has a step-by-step breakdown of the bioinformatics pipeline, including the software used, inputs, outputs, and specific files for this publication.

Software Repositories, Resources, and Tools used in this project:

• ABRICATE
• AMRFinderPlus
• Center for Genomic Epidemiology
• EcMLST
• FastQC
• MLST
• MultiQC
• PointFinder
• Prokka
• QUAST
• ResFinder
• SRAtools
• SPAdes
• StarAMR
• Trimmomatic
• Whittham MLST Scheme