{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:19Z","timestamp":1753875859966,"version":"3.41.2"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2024,12,2]],"date-time":"2024-12-02T00:00:00Z","timestamp":1733097600000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"US National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["U19AI110818","U01AI151812"],"award-info":[{"award-number":["U19AI110818","U01AI151812"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, and detection of superinfections and recombination events. While sample barcoding methods exist to track inter-sample contamination, they are not always used and can only detect contamination in the experimental pipeline from the point they are added. The underlying genomic information in a sample, however, carries information about inter-sample contamination occurring at any stage. Here, we present Polyphonia, a tool for detecting inter-sample contamination directly from deep sequencing data without the need for additional controls, using intrahost variant frequencies. We apply Polyphonia to 1102 SARS-CoV-2 samples sequenced at the Broad Institute and already tracked using molecular barcoding for comparison.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Polyphonia is available as a standalone Docker image and is also included as part of viral-ngs, available in Dockstore. Full documentation, source code, and instructions for use are available at https:\/\/github.com\/broadinstitute\/polyphonia.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae698","type":"journal-article","created":{"date-parts":[[2024,12,14]],"date-time":"2024-12-14T11:51:57Z","timestamp":1734177117000},"source":"Crossref","is-referenced-by-count":1,"title":["Polyphonia: detecting inter-sample contamination in viral genomic sequencing data"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4163-706X","authenticated-orcid":false,"given":"Lydia A","family":"Krasilnikova","sequence":"first","affiliation":[{"name":"Howard Hughes Medical Institute , Chevy Chase, MD 20815,","place":["United States"]},{"name":"Infectious Disease and Microbiome Program, Broad Institute , Cambridge, MA 02142,","place":["United States"]},{"name":"Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9114-6421","authenticated-orcid":false,"given":"Christopher H","family":"Tomkins-Tinch","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute , Cambridge, MA 02142,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2411-0621","authenticated-orcid":false,"given":"Alton C","family":"Gayton","sequence":"additional","affiliation":[{"name":"Department of Virology, Harvard Medical School, Harvard University , Cambridge, MA 02138,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6699-3568","authenticated-orcid":false,"given":"Stephen F","family":"Schaffner","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute , Cambridge, MA 02142,","place":["United States"]},{"name":"Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138,","place":["United States"]},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University , Boston, MA 02115,","place":["United States"]}]},{"given":"Sabrina T","family":"Dobbins","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute , Cambridge, MA 02142,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6307-0012","authenticated-orcid":false,"given":"Adrianne","family":"Gladden-Young","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Microbiology, Tufts University Graduate School of Biomedical Sciences , Boston, MA 02111,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1799-7295","authenticated-orcid":false,"given":"Katherine J","family":"Siddle","sequence":"additional","affiliation":[{"name":"Department of Molecular Microbiology and Immunology, Brown University , Providence, RI 02912,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7226-7781","authenticated-orcid":false,"given":"Daniel J","family":"Park","sequence":"additional","affiliation":[{"name":"Infectious Disease and Microbiome Program, Broad Institute , Cambridge, MA 02142,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9843-1890","authenticated-orcid":false,"given":"Pardis C","family":"Sabeti","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute , Chevy Chase, MD 20815,","place":["United States"]},{"name":"Infectious Disease and Microbiome Program, Broad Institute , Cambridge, MA 02142,","place":["United States"]},{"name":"Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138,","place":["United States"]},{"name":"Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University , Boston, MA 02115,","place":["United States"]},{"name":"Massachusetts Consortium for Pathogen Readiness , Boston, MA 02115,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2024,12,2]]},"reference":[{"key":"2024122715472437700_btae698-B1","doi-asserted-by":"crossref","first-page":"2601","DOI":"10.1093\/bioinformatics\/btr446","article-title":"ContEst: estimating cross-contamination of human samples in next-generation sequencing data","volume":"27","author":"Cibulskis","year":"2011","journal-title":"Bioinformatics"},{"key":"2024122715472437700_btae698-B2","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"year":"2020","author":"De 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