Mapache: a flexible pipeline to map ancient DNA

TL;DR

Mapache is a scalable, automated pipeline designed to efficiently map, quantify, and impute ancient and modern DNA, addressing the challenges of reproducibility and resource consumption in large-scale genomic studies.

Contribution

It introduces a flexible, robust, and scalable Snakemake-based pipeline specifically optimized for ancient DNA mapping and analysis.

Findings

Efficient handling of large ancient DNA datasets.

Reproducible mapping and imputation workflows.

Optimized for low-space consumption.

Abstract

Summary: Mapping ancient DNA to a reference genome is challenging as it involves numerous steps, is time-consuming and has to be repeated within a study to assess the quality of extracts and libraries; as a result, the mapping needs to be automatized to handle large amounts of data in a reproducible way. We present mapache, a flexible, robust, and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large data sets such as reference panels and multiple extracts and libraries.