Mapache: a flexible pipeline to map ancient DNA

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  • Samuel Neuenschwander
  • Diana I Cruz Dávalos
  • Lucas Anchieri
  • Bárbara Sousa da Mota
  • Davide Bozzi
  • Simone Rubinacci
  • Olivier Delaneau
  • Rasmussen, Simon
  • Anna-Sapfo Malaspinas

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 ( An extensive manual is provided at

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original languageEnglish
JournalBioinformatics (Online)
Issue number2
Number of pages3
Publication statusPublished - 2023

Bibliographical note

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

    Research areas

  • Software, DNA, Ancient, Genome, Workflow

ID: 346589617