Pavian

Pavian provides analysis and visualization of metagenomic taxonomic classification results to support pathogen identification in infectious disease and microbial ecology studies.

Key Features:

• Integration with Kraken and Centrifuge: Accepts and analyzes classification outputs from the Kraken and Centrifuge metagenomic classifiers.
• Interactive data visualization: Generates tables, heatmaps, and flow diagrams to analyze, display, and transform metagenomic data.
• Alignment viewer for validation: Displays alignments against specific genomes to validate classifier matches and confirm taxonomic assignments.
• Contaminant and host filtering: Enables identification and filtering of host DNA, laboratory contaminants, and non-pathogenic microbiota from metagenomic results.

Scientific Applications:

• Infectious disease research and diagnosis: Supports identification of pathogenic organisms from metagenomic samples to inform diagnostic interpretation.
• Microbial community analysis: Facilitates profiling and visualization of microbial communities and potential pathogens in complex samples.
• Validation of taxonomic assignments: Enables confirmation of classifier-derived hits through genome-specific alignment inspection.

Methodology:

Implemented in the R programming language.