Tau-typing

Tau-typing identifies genomic regions whose phylogenetic signal best reflects genome-wide relationships to enable marker-based molecular typing and evolutionary analysis of microorganisms.

Key Features:

• Phylogenetic Marker Identification: Discerns genes or genomic segments whose phylogenetic resolution aligns with genome-wide resolving power to support molecular typing and classification of microbial species.
• Kendall Tau Rank Correlation Statistic: Uses the Kendall Tau rank correlation to assess and select genomic regions that are most representative of genome-wide phylogenetic relationships.
• Nextflow Implementation: Implements the analysis pipeline in Nextflow for workflow management and scalable execution.
• Containerization with Docker and Singularity: Packages components in Docker and Singularity containers to provide consistent computational environments.
• Scalability and Reproducibility: Leverages workflow management and containerization to support scalable and reproducible analyses across computing platforms.

Scientific Applications:

• Molecular typing when whole-genome sequencing is infeasible: Enables marker-based molecular typing for organisms where whole-genome sequencing is impractical due to cost or scalability constraints.
• Studies of protozoan parasites and unculturable microorganisms: Supports evolutionary and phylogenetic studies of protozoan parasites and other microorganisms that cannot be easily cultured by identifying informative loci without comprehensive genome sequencing.

Methodology:

Input genomes are evaluated by computing the Kendall Tau rank correlation between individual genes or genomic segments and the whole-genome phylogenetic signal to identify regions that best reflect genome-wide relationships; the pipeline is implemented in Nextflow and distributed via Docker and Singularity containers.