{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T06:35:01Z","timestamp":1770273301222,"version":"3.49.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T00:00:00Z","timestamp":1767916800000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"BWF grant"},{"name":"Miller Institute in Basic Research Science at University of California, Berkeley and the Novo Nordisk Hallas-M\u00f8ller Emerging","award":["NNF24OC0088862"],"award-info":[{"award-number":["NNF24OC0088862"]}]},{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Koret-UC Berkeley-Tel Aviv University Initiative in Computational Biology and Bioinformatics"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Sediment DNA\u2014the recovery of genetic material from archaeological sediments\u2014is an exciting new frontier in ancient DNA research, offering the potential to study individuals at a given archaeological site without destructive sampling. In recent years, several studies have demonstrated the promise of this approach by extracting hominin DNA from prehistoric sediments, including those dating back to the Middle or Late Pleistocene. However, a lack of open-source workflows for analysis of hominin sediment DNA samples poses a challenge for data processing and reproducibility of findings across studies. Here, we introduce a snakemake workflow, sedimix, for processing genomic sequences from archaeological sediment DNA samples to identify hominin sequences and generate relevant summary statistics to assess the reliability of the pipeline. By performing simulations and comparing our results to two published studies with human DNA from \u223c25,000\u2009years ago (including shotgun data from a sediment sample and capture data from touch DNA recovered from a deer tooth pendant) we demonstrate that sedimix yields accurate and reliable inferences. sedimix offers a reliable and adaptable framework to aid in the analysis of sediment DNA datasets and improve reproducibility across studies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>sedimix is available as an open-source software with the associated code, example data, and user manual with installation instructions available at https:\/\/github.com\/jierui-cell\/sedimix. A permanent archived version of this release is available via Zenodo: https:\/\/doi.org\/10.5281\/zenodo.17244854.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag004","type":"journal-article","created":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T12:39:34Z","timestamp":1767875974000},"source":"Crossref","is-referenced-by-count":0,"title":["<i>sedimix<\/i>\n                    : a workflow for the analysis of hominin nuclear DNA sequences from sediments"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1146-3775","authenticated-orcid":false,"given":"Jierui","family":"Xu","sequence":"first","affiliation":[{"name":"University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7687-5370","authenticated-orcid":false,"given":"Elena I","family":"Zavala","sequence":"additional","affiliation":[{"name":"University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,","place":["United States"]}]},{"given":"Priya","family":"Moorjani","sequence":"additional","affiliation":[{"name":"University of California, Berkeley Department of Molecular and Cell Biology, , Berkeley, CA, 94720,","place":["United States"]},{"name":"University of California, Berkeley Center for Computational Biology, , Berkeley, CA, 94720,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2026,1,9]]},"reference":[{"key":"2026020310414884800_btag004-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"1000 Genomes Project Consortium","year":"2015","journal-title":"Nature"},{"key":"2026020310414884800_btag004-B2","first-page":"4724","article-title":"The half-life of DNA in bone: measuring decay kinetics in 158 dated 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