mapache

mapache performs mapping, quantification, and imputation of ancient and present-day DNA to support genomic analyses, including re-mapping reference panels and processing multiple extracts and libraries per sample against one or several genomes.

Key Features:

• Mapping, quantification, and imputation: Performs mapping, quantification, and genotype imputation for sequencing data from ancient and present-day samples.
• Integration with Snakemake: Operates within the Snakemake workflow manager to enable modular workflows and reproducibility.
• Low-space consumption: Optimized for reduced disk-space usage when handling large datasets and re-mapping extensive reference panels.
• Scalability: Scales to process large datasets and multiple genomes without compromising analytical throughput.
• Multi-extract and multi-library handling: Supports processing multiple extracts and libraries per sample against one or several reference genomes.

Scientific Applications:

• Ancient DNA analysis: Provides a reproducible framework for mapping and analyzing DNA from historical and archaeological samples, including quantification and imputation.
• Present-day DNA analysis: Supports mapping, quantification, and imputation of modern sequencing datasets.
• Evolutionary biology: Enables analyses that inform evolutionary relationships and population history using mapped and imputed genomic data.
• Archaeogenetics: Facilitates genetic investigation of archaeological specimens through standardized mapping and downstream analyses.
• Population genetics: Supports generation of mapped and imputed datasets for population-level inference and comparative analyses.

Methodology:

Uses the Snakemake workflow manager with a modular approach to ensure reproducibility, enables re-mapping of large reference panels, processes multiple extracts and libraries per sample against one or several genomes, and is optimized for low disk-space consumption.