Mapache: a flexible pipeline to map ancient DNA.

ABSTRACT

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.