{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/mapache-a-flexible-pipeline-to-map-ancient","title":"Mapache: a flexible pipeline to map ancient DNA","arxiv_id":"2208.13283","date":"2022-08-28","proceeding":null,"authors":["Samuel Neuenschwander","Diana I. Cruz Dávalos","Lucas Anchieri","Bárbara Sousa da Mota","Davide Bozzi","Simone Rubinacci","Olivier Delaneau","Simon Rasmussen","Anna-Sapfo Malaspinas"],"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.","url_abs":"https://arxiv.org/abs/2208.13283v1","url_pdf":"https://arxiv.org/pdf/2208.13283v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"mapache-a-flexible-pipeline-to-map-ancient","repo_url":"https://github.com/sneuensc/mapache","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}