Polyphonia

Polyphonia detects inter-sample contamination in viral genomic sequencing data by utilizing intrahost variant frequencies without requiring additional controls.

Key Features:

• Contamination Detection from Deep Sequencing Data: Polyphonia identifies inter-sample contamination directly from deep sequencing data without the need for additional controls.
• Intrahost Variant Frequency Analysis: Polyphonia uses intrahost variant frequencies to detect contamination, leveraging the underlying genomic information present in samples.
• Contamination Detection at Any Stage: Polyphonia detects inter-sample contamination occurring at any stage of the process, unlike sample barcoding methods that can only detect contamination from the point they are added.

Scientific Applications:

• Variant Detection Quality Control: Polyphonia helps ensure accurate variant detection by identifying inter-sample contamination that can confound results.
• Within-Host Evolution Analysis: Polyphonia supports accurate analysis of within-host evolution by removing contaminated samples.
• Outbreak Reconstruction: Polyphonia improves outbreak reconstruction by detecting contamination that could distort transmission patterns.
• Superinfection Detection: Polyphonia aids in detecting superinfections by distinguishing true mixed infections from contamination artifacts.
• Recombination Event Detection: Polyphonia facilitates accurate detection of recombination events by filtering out contaminated samples.
• SARS-CoV-2 Surveillance: Polyphonia has been applied to 1102 SARS-CoV-2 samples sequenced at the Broad Institute for contamination detection.

Methodology:

Polyphonia uses intrahost variant frequencies from deep sequencing data to detect inter-sample contamination.