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Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing.

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Title: Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing.
Authors: Lee ER; National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada., Parkin N; Data First Consulting Inc., Belmont, California, USA., Jennings C; Virology Quality Assurance Program, Rush Medical College, Chicago, USA., Brumme CJ; British Columbia Center for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada., Enns E; Bioinformatics Core at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada., Casadellà M; IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain., Howison M; Research Improving People's Lives, Providence, Rhode Island, USA., Coetzer M; Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island, USA., Avila-Rios S; Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico., Capina R; National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada., Marinier E; Bioinformatics Core at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada., Van Domselaar G; Bioinformatics Core at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada., Noguera-Julian M; IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain., Kirkby D; British Columbia Center for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada., Knaggs J; British Columbia Center for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada., Harrigan R; Division of AIDS, Department of Medicine, University of British Columbia, Vancouver, Canada., Quiñones-Mateu M; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand., Paredes R; IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain.; Infectious Diseases Service, Hospital Germans Trias, Badalona, Catalonia, Spain., Kantor R; Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island, USA., Sandstrom P; National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada., Ji H; National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada. hezhao.ji@canada.ca.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada. hezhao.ji@canada.ca.
Source: Scientific reports [Sci Rep] 2020 Jan 31; Vol. 10 (1), pp. 1634. Date of Electronic Publication: 2020 Jan 31.
Publication Type: Comparative Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Journal Info: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE
Database: MEDLINE Ultimate
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  Data: Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing.
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  Data: <searchLink fieldCode="AU" term="%22Lee+ER%22">Lee ER</searchLink>; National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.<br /><searchLink fieldCode="AU" term="%22Parkin+N%22">Parkin N</searchLink>; Data First Consulting Inc., Belmont, California, USA.<br /><searchLink fieldCode="AU" term="%22Jennings+C%22">Jennings C</searchLink>; Virology Quality Assurance Program, Rush Medical College, Chicago, USA.<br /><searchLink fieldCode="AU" term="%22Brumme+CJ%22">Brumme CJ</searchLink>; British Columbia Center for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.<br /><searchLink fieldCode="AU" term="%22Enns+E%22">Enns E</searchLink>; Bioinformatics Core at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.<br /><searchLink fieldCode="AU" term="%22Casadellà+M%22">Casadellà M</searchLink>; IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain.<br /><searchLink fieldCode="AU" term="%22Howison+M%22">Howison M</searchLink>; Research Improving People's Lives, Providence, Rhode Island, USA.<br /><searchLink fieldCode="AU" term="%22Coetzer+M%22">Coetzer M</searchLink>; Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island, USA.<br /><searchLink fieldCode="AU" term="%22Avila-Rios+S%22">Avila-Rios S</searchLink>; Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico.<br /><searchLink fieldCode="AU" term="%22Capina+R%22">Capina R</searchLink>; National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.<br /><searchLink fieldCode="AU" term="%22Marinier+E%22">Marinier E</searchLink>; Bioinformatics Core at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.<br /><searchLink fieldCode="AU" term="%22Van+Domselaar+G%22">Van Domselaar G</searchLink>; Bioinformatics Core at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.<br /><searchLink fieldCode="AU" term="%22Noguera-Julian+M%22">Noguera-Julian M</searchLink>; IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain.<br /><searchLink fieldCode="AU" term="%22Kirkby+D%22">Kirkby D</searchLink>; British Columbia Center for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.<br /><searchLink fieldCode="AU" term="%22Knaggs+J%22">Knaggs J</searchLink>; British Columbia Center for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.; Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.<br /><searchLink fieldCode="AU" term="%22Harrigan+R%22">Harrigan R</searchLink>; Division of AIDS, Department of Medicine, University of British Columbia, Vancouver, Canada.<br /><searchLink fieldCode="AU" term="%22Quiñones-Mateu+M%22">Quiñones-Mateu M</searchLink>; Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.<br /><searchLink fieldCode="AU" term="%22Paredes+R%22">Paredes R</searchLink>; IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain.; Infectious Diseases Service, Hospital Germans Trias, Badalona, Catalonia, Spain.<br /><searchLink fieldCode="AU" term="%22Kantor+R%22">Kantor R</searchLink>; Division of Infectious Diseases, Brown University Alpert Medical School, Providence, Rhode Island, USA.<br /><searchLink fieldCode="AU" term="%22Sandstrom+P%22">Sandstrom P</searchLink>; National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.<br /><searchLink fieldCode="AU" term="%22Ji+H%22">Ji H</searchLink>; National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, Manitoba, Canada. hezhao.ji@canada.ca.; Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada. hezhao.ji@canada.ca.
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  Data: <searchLink fieldCode="JN" term="%22101563288%22">Scientific reports</searchLink> [Sci Rep] 2020 Jan 31; Vol. 10 (1), pp. 1634. <i>Date of Electronic Publication: </i>2020 Jan 31.
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