PHAT

PHAT processes and analyzes next-generation sequencing (NGS) data to elucidate relationships between pathogens and their hosts.

Key Features:

• NGS data handling: Accepts raw and aligned sequence files together with reference data inputs for pathogen-host analyses.
• Quality control (QC) reporting: Generates comprehensive QC reports to assess integrity and reliability of sequencing data.
• Alignment: Performs sequence alignment for downstream comparative analyses.
• Variant calling: Identifies genetic variations between pathogens and hosts through variant calling procedures.
• Linear and circular alignment viewing: Supports visualization of both linear and circular genomic alignment structures.
• Output formats: Produces graphical and tabular outputs for visualization and detailed analysis.
• Integrated analysis pipeline: Provides an integrative platform that streamlines the analysis pipeline and reduces the need for custom scripting.

Scientific Applications:

• Pathogen-host relationship analysis: Elucidates interactions and relationships between pathogens and their hosts using NGS data.
• Variant discovery between pathogen and host: Identifies genetic variations relevant to pathogen-host comparisons.
• Genomic structure visualization: Visualizes linear and circular genomes encountered in pathogen-host studies, such as viral or plasmid genomes.
• Sequencing data quality assessment: Enables QC-based evaluation prior to downstream analyses.

Methodology:

Processes NGS data by accepting raw and aligned sequence files with reference inputs, performing quality control reporting, executing alignment and variant calling, and generating linear and circular alignment views as graphical and tabular outputs.