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

doi:10.1093/bioinformatics/btad028

Mapache: a flexible pipeline to map ancient DNA

Bioinformatics. 2023 Feb 3;39(2):btad028. doi: 10.1093/bioinformatics/btad028.

Authors

Samuel Neuenschwander^{1

2}, Diana I Cruz Dávalos^{1

3}, Lucas Anchieri^{1

3}, Bárbara Sousa da Mota^{1

3}, Davide Bozzi^{1

3}, Simone Rubinacci^{1

3}, Olivier Delaneau^{1

3}, Simon Rasmussen⁴, Anna-Sapfo Malaspinas^{1

3}

Affiliations

¹ Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland.
² Vital-IT, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
³ Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
⁴ Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA, Ancient*
Genome
Software*
Workflow

Substances

DNA, Ancient

Abstract

Publication types

MeSH terms

Substances

Grants and funding