DamageProfiler

DamageProfiler calculates damage profiles from mapped reads in ancient DNA (aDNA) samples to quantify deamination and fragmentation patterns for authentication and downstream analyses.

Key Features:

• Damage profiling: Calculates damage profiles from mapped reads to characterize nucleotide misincorporation and fragmentation patterns in aDNA.
• Output formats: Produces graphical plots and text-based summaries and exports results in multiple file formats for further processing.
• aDNA damage characterization: Quantifies deamination and fragmentation signatures characteristic of ancient DNA.
• Authentication support: Provides damage-pattern information to help distinguish genuine ancient sequences from modern contaminants.
• Implementation: Provided as a Java-based application.

Scientific Applications:

• Ancient DNA authentication: Assessing damage patterns to authenticate aDNA samples and evaluate contamination.
• Damage quantification: Quantifying deamination and fragmentation to characterize aDNA degradation.
• Data preparation for downstream analyses: Generating damage profiles and outputs that inform subsequent processing and interpretation of aDNA data.

Methodology:

Computes damage profiles from mapped reads and generates graphical plots and text-based summaries.