  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.
