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arXiv · 2208.13283

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
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Abstract

Summary: Mapping ancient DNA to a reference genome is challenging as it involves numerous steps, is time-consuming and has to be repeated within a study to assess the quality of extracts and libraries; as a result, the mapping needs to be automatized to handle large amounts of data in a reproducible way. We present 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 data sets such as reference panels and multiple extracts and libraries.

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Samuel Neuenschwander, Diana I. Cruz Dávalos, Lucas Anchieri, Bárbara Sousa da Mota, Davide Bozzi, Simone Rubinacci, Olivier Delaneau, Simon Rasmussen, Anna-Sapfo Malaspinas. 2022-08-28. Mapache: a flexible pipeline to map ancient DNA. https://doi.org/10.1093/bioinformatics%2Fbtad028

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