Mapache: a flexible pipeline to map ancient DNA

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

Research output: Contribution to journalJournal articleResearchpeer-review

5 Citations (Scopus)
13 Downloads (Pure)

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.

Original languageEnglish
JournalBioinformatics (Online)
Volume39
Issue number2
Number of pages3
ISSN1367-4811
DOIs
Publication statusPublished - 2023

Bibliographical note

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

Keywords

  • Software
  • DNA, Ancient
  • Genome
  • Workflow

Cite this