sedimix: A workflow for the analysis of hominin nuclear DNA sequences from sediments.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41512286", "kind": "science-record", "revision": 3, "content_hash": "sha256:6ea4bdc642b5f4c998a1014dad1c61fe8fc061e8940393580435a75014a435e4", "created_at": "2026-11-01T20:31:29Z", "updated_at": "2026-11-01T22:15:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "sedimix: A workflow for the analysis of hominin nuclear DNA sequences from sediments.", "doi": "10.1093/bioinformatics/btag004", "pmid": "41512286", "authors": ["Jierui Xu", "Elena I Zavala", "Priya Moorjani"], "journal": "Bioinformatics (Oxford, England)", "year": 2026, "abstract": "SUMMARY: Sediment DNA--the ability to extract DNA from archaeological sediments-- is 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 recovering 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 ∼25,000 years 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.\nAVAILABILITY AND IMPLEMENTATION: 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.\nSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.", "claims": [{"id": "claim-method", "statement": "We evaluated the performance by measuring two metrics: sensitivity defined as the number of identified reads that were correctly classified as “hominin” (Neanderthal or modern human) divided by the total number of hominin reads simulated, and precision defined as the number of identified reads that were truly hominin divided by the total number of identified reads.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41512286", "locator": "sections[3] \"3 Results\" paragraph 2", "quote": "We evaluated the performance by measuring two metrics: sensitivity defined as the number of identified reads that were correctly classified as “hominin” (Neanderthal or modern human) divided by the total number of hominin reads simulated, and precision defined as the number of identified reads that were truly hominin divided by the total number of identified reads."}], "state": "complete"}, {"id": "claim-data-access", "statement": "There are no new data associated with this article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41512286", "locator": "sections[9] \"Data availability\" paragraph 2", "quote": "There are no new data associated with this article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Across the three simulated datasets, sedimix achieved sensitivities of 94.1%, 94.1%, and 94.7% and precisions of 100%, 100%, and 97.5%, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41512286", "locator": "sections[3] \"3 Results\" paragraph 4", "quote": "Specifically, across the three simulated datasets, we achieved a sensitivity of 94.1%, 94.1%, and 94.7%, and a precision of 100%, 100%, 97.5%, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Across the three simulated datasets, sedimix achieved sensitivities of 94.1%, 94.1%, and 94.7% and precisions of 100%, 100%, and 97.5%, respectively.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41512286"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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