EAGER

EAGER performs reconstruction and analysis of ancient genomes from sequencing data, enabling preprocessing of ancient DNA reads, mapping to reference genomes, authentication to detect and minimize contamination, and discovery and analysis of genetic variants for evolutionary and population studies.

Key Features:

• Preprocessing: Tailored preprocessing for ancient DNA samples to prepare sequencing reads for downstream analysis.
• Mapping and Authentication: Maps reads to reference genomes and incorporates authentication steps to verify ancient DNA and reduce modern contamination.
• Quality Assessment: Provides tools to assess the quality and integrity of ancient DNA samples.
• Genotyping and Variant Analysis: Discovers, filters, and analyzes genetic variants in ancient genomes to support genotyping and downstream analyses.
• Integration of Tools and Methods: Integrates established bioinformatics tools and novel methodologies developed specifically for ancient DNA analysis.
• Large-scale Dataset Processing: Processes large-scale ancient genomic sequencing datasets.

Scientific Applications:

• Human history and evolution: Enables studies of human history, evolution, and genetic diversity over time.
• Population dynamics and migration: Supports inference of population dynamics and historical migration patterns.
• Interdisciplinary research: Facilitates integration of genetic data with archaeology and anthropology to reconstruct past environments and evolutionary pressures.

Methodology:

Preprocessing of sequencing reads, mapping to reference genomes, authentication of ancient DNA to assess contamination, quality assessment, variant discovery, filtering, and variant analysis, with integration of established and novel aDNA-specific tools.