biostudies-literatureNeuenschwander SNovo Nordisk FoundationSwiss National Science FoundationNovo Nordisk Foundation Center for Protein Researchbtad028https://www.ebi.ac.uk/biostudies/studies/S-EPMC9901408biostudies-literatureUnknown39(2)<h4>Summary</h4>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.<h4>Availability and implementation</h4>Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.Bioinformatics (Oxford, England)Mapache: a flexible pipeline to map ancient DNA.PMC9901408PCEGP3_181251PI Simon Rasmussen181251Sousa da Mota BNeuenschwander SBozzi DRasmussen SAnchieri LRubinacci SCruz Davalos DIMalaspinas ASDelaneau OfalseMapache: a flexible pipeline to map ancient DNA.<h4>Summary</h4>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.<h4>Availability and implementation</h4>Mapache is freely available on GitHub (https://github.com/sneuensc/mapache). An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.2023-01-01T00:00:00Z2023 Feb2026-04-07T13:36:11.771Z2025-02-19T00:12:18.243ZS-EPMC99014083663719710.1093/bioinformatics/btad028