TransFlow

TransFlow performs transmission analysis of Mycobacterium tuberculosis (MTB) using whole-genome sequencing (WGS) data to identify transmission clusters, reconstruct transmission networks, and infer transmission-associated risk factors.

Key Features:

• Comprehensive workflow: Implements quality control, sequence alignment, variant calling, transmission clustering, network reconstruction, and risk factor inference for MTB WGS data.
• MTB WGS support: Operates specifically on whole-genome sequencing (WGS) data from Mycobacterium tuberculosis (MTB).
• Workflow management and reproducibility: Uses Snakemake for workflow management and Conda for dependency resolution to enable scalable and reproducible processing.
• Data visualization and reporting: Produces summary statistics, visualizations, and detailed analytical reports for interpretation of results.

Scientific Applications:

• Epidemiological studies: Enables analysis of MTB transmission dynamics from WGS data.
• Outbreak detection and cluster identification: Identifies transmission clusters and reconstructs transmission networks for outbreak investigation.
• Public health risk factor inference: Supports inference of risk factors associated with TB transmission to inform public health interventions.

Methodology:

Processes raw sequencing data through quality control, sequence alignment, variant calling, clustering analysis, transmission network reconstruction, and risk factor inference, using Snakemake for workflow management and Conda for dependency resolution.