{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T18:35:59Z","timestamp":1772562959658,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,2,7]],"date-time":"2023-02-07T00:00:00Z","timestamp":1675728000000},"content-version":"vor","delay-in-days":25,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"SNSF","doi-asserted-by":"publisher","award":["PCEGP3_181251"],"award-info":[{"award-number":["PCEGP3_181251"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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\u2014such as reference panels and multiple extracts and libraries per sample \u2014 to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Mapache is freely available on GitHub (https:\/\/github.com\/sneuensc\/mapache). An extensive manual is provided at https:\/\/github.com\/sneuensc\/mapache\/wiki.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad028","type":"journal-article","created":{"date-parts":[[2023,1,14]],"date-time":"2023-01-14T01:26:39Z","timestamp":1673659599000},"source":"Crossref","is-referenced-by-count":18,"title":["Mapache: a flexible pipeline to map ancient DNA"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4080-5546","authenticated-orcid":false,"given":"Samuel","family":"Neuenschwander","sequence":"first","affiliation":[{"name":"Department of Computational Biology, University of Lausanne , Lausanne 1015, Switzerland"},{"name":"Vital-IT, Swiss Institute of Bioinformatics , Lausanne 1015, 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