IPD-pipeline

IPD-pipeline performs comprehensive analysis of pathogen genomic NGS datasets, including short and long reads, to quantify pathogen presence, detect mutations, assign SARS-CoV-2 clades, and infer phylogenetic relationships for outbreak monitoring.

Key Features:

• Integrated analysis of heterogeneous NGS data: Processes short- and long-read sequencing datasets to provide uniform quantitative, variant, and phylogenetic analyses across platforms.
• Pathogen quantification and mutation analysis: Quantifies the presence of over 1,060 pathogens in sequencing data and performs detailed mutation and variant analysis.
• SARS-CoV-2 specific module: Includes a dedicated SARS-CoV-2 module for viral clade assignment and identification of novel variants.
• Phylogenetic analysis: Establishes phylogenetic connections among genome isolates to support evolutionary and transmission inference.
• Automated report generation: Produces automated reports summarizing quantitative, variant, and phylogenetic results.

Scientific Applications:

• SARS-CoV-2 genomic surveillance: Quantifies transcript burdens and identifies thousands of variants, including novel variants, across SARS-CoV-2 datasets.
• Outbreak investigation and transmission tracing: Uses phylogenetic relationships among isolates to trace transmission patterns and outbreak sources.
• Broad pathogen monitoring: Enables quantification and variant analysis across heterogeneous NGS datasets to support public health laboratory surveillance of multiple pathogens.

Methodology:

Processes heterogeneous short- and long-read NGS data to quantify pathogen genomes (>1,060 pathogens), perform integrated variant/mutation analysis, assign SARS-CoV-2 clades, conduct phylogenetic analyses, and generate automated reports.