Mapache: a flexible pipeline to map ancient DNA

We introduce 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 datasets-such as reference panels and multiple extracts and libraries per sample- to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools.