MapDamage

MapDamage analyzes and quantifies patterns of DNA damage in ancient DNA (aDNA) next-generation sequencing reads to characterize nucleotide misincorporation and fragmentation signatures and assess authenticity of endogenous fragments versus contaminant sequences.

Key Features:

• Nucleotide Misincorporation Analysis: Calculates nucleotide misincorporations by analyzing next-generation sequencing reads mapped against a reference genome to identify deamination and other chemical modifications.
• Fragmentation Signature Detection: Evaluates fragmentation patterns of DNA fragments to characterize aDNA degradation signatures.
• Perl-based Computational Processing: Employs Perl scripts to compute misincorporation and fragmentation signatures from mapped sequencing reads.
• R Integration for Pattern Recognition: Processes computed misincorporation and fragmentation data with an embedded R script to detect typical aDNA damage patterns.
• Authentication of Endogenous DNA: Distinguishes endogenous aDNA fragments from contaminant sequences, including environmental microbial contaminants, based on damage profiles.

Scientific Applications:

• Paleogenomics: Profiles and authenticates aDNA used in paleogenomic reconstructions of past organisms and populations.
• Archaeology: Validates ancient DNA sequences from archaeological samples to support historical and cultural genetic analyses.
• Evolutionary Biology: Assesses sequence authenticity for studies of evolutionary processes and lineage histories.
• Contamination Assessment and Authentication: Differentiates genuine aDNA from modern contamination to ensure reliability of downstream analyses.
• Phylogenetics and Genome Reconstruction: Informs phylogenetic analyses and reconstruction of historical genomes by validating input sequence data.

Methodology:

Analyzes next-generation sequencing reads mapped to a reference genome, computes nucleotide misincorporation and fragmentation signatures using Perl scripts, and processes these results with an embedded R script for damage-pattern recognition.