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Updated: Aug 14, 2025

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
Published on: September 3, 2009
Mapache: a flexible pipeline to map ancient DNA
Samuel Neuenschwander1,2, Diana I Cruz Dávalos1,3, Lucas Anchieri1,3
1Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.
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.
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