Mapache: a flexible pipeline to map ancient DNA

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—s...

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Detalles Bibliográficos
Autores principales: Neuenschwander, Samuel, Cruz Dávalos, Diana I, Anchieri, Lucas, Sousa da Mota, Bárbara, Bozzi, Davide, Rubinacci, Simone, Delaneau, Olivier, Rasmussen, Simon, Malaspinas, Anna-Sapfo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9901408/
https://www.ncbi.nlm.nih.gov/pubmed/36637197
http://dx.doi.org/10.1093/bioinformatics/btad028
Descripción
Sumario: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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