Polyphonia: detecting inter-sample contamination in viral genomic sequencing data.

Autor:	Krasilnikova LA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States.; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, United States.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States., Tomkins-Tinch CH; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, United States., Gayton AC; Department of Virology, Harvard Medical School, Harvard University, Cambridge, MA 02138, United States., Schaffner SF; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, United States.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, United States., Dobbins ST; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, United States., Gladden-Young A; Department of Molecular Biology and Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, United States., Siddle KJ; Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, United States., Park DJ; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, United States., Sabeti PC; Howard Hughes Medical Institute, Chevy Chase, MD 20815, United States.; Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, United States.; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States.; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, United States.; Massachusetts Consortium for Pathogen Readiness, Boston, MA 02115, United States.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2024 Nov 28; Vol. 40 (12).
DOI:	10.1093/bioinformatics/btae698
Abstrakt:	Summary: 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. Availability and Implementation: 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. (© The Author(s) 2024. Published by Oxford University Press.)
Databáze:	MEDLINE
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