Summary

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.

Availability and implementation

Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.

Supplementary information

Supplementary data are available at Bioinformatics online.

© The Author(s) 2023. Published by Oxford University Press.
2023
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