THRESHER

THRESHER is a bacterial genomics toolkit with three core functionalities:

• Strain Identifier: Identifies strains/transmission clusters using phylothresholds (phylogenetically-corrected SNP thresholds).

• Genome Profiler: Infers substitution probabilities and mobile genetic element (MGE) dynamics leveraging publicly available genomes.

• Evolution Simulator: Models bacterial evolution through substitution, gene gain/loss, and recombination events.

Workflow

Strain Identifier

• Full Pipeline
• Redo Endpoint Elements highlighted in green (#91a01e) indicate updates applied to existing results.
• New SNPs Elements highlighted in green (#91a01e) indicate updates applied to existing results.
• New Full Elements highlighted in green (#91a01e) indicate updates applied to existing results.

Genome Profiler

Evolution Simulator

Documentation

Getting Started

• System Requirements
• Installation
• Quick Start

Core Functionalities

• Strain Identifier
  • Full Pipeline Mode
  • Redo Endpoint Mode
  • New SNPs Mode
  • New Full Mode
• Genome Profiler
• Evolution Simulator

Advanced Usage

• Conda Environment Management
• Resuming Interrupted Runs

Development Status

Please be advised that this pipeline is still in its early development stage. It is subject to significant changes in terms of options, outputs, and other functionalities. Users should be prepared for potential modifications and updates in future releases.

Authors

Qianxuan (Sean) She

Acknowledgments

Developed under the mentorship of:

Dr. Paul J. Planet
Email: planetp@chop.edu

Dr. Ahmed M. Moustafa
Email: moustafaam@chop.edu

Dr. Joseph P. Zackular
Email: joseph.zackular@pennmedicine.upenn.edu