HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities

• Lajos Kalmar,

  Roles Data curation, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0003-3691-8350

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• Srishti Gupta,

  Roles Formal analysis, Methodology, Visualization, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0001-6721-1783

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• Iain R. L. Kean,

  Roles Formal analysis, Investigation, Visualization, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0003-1066-8285

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• Xiaoliang Ba,

  Roles Investigation, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0002-3882-3585

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• Nazreen Hadjirin,

  Roles Investigation, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

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• Elizabeth M. Lay,

  Roles Investigation

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

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• Stefan P. W. de Vries,

  Roles Formal analysis, Investigation, Methodology, Supervision, Writing – review & editing

  Current address: MSD Animal Health, Boxmeer, The Netherlands

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0002-0823-208X

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• Michael Bateman,

  Roles Formal analysis, Methodology, Software, Writing – review & editing

  Current address: Arthur D. Little, New Fetter Place West, London, United Kingdom

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

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• Harriet Bartlet,

  Roles Investigation, Resources

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0002-7389-8785

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• Juan Hernandez-Garcia,

  Roles Investigation, Resources

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0001-5932-9327

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• Alexander W. Tucker,

  Roles Conceptualization, Funding acquisition, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0003-0062-0843

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• Olivier Restif,

  Roles Conceptualization, Formal analysis, Funding acquisition, Methodology, Writing – original draft, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0001-9158-853X

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• Mark P. Stevens,

  Roles Conceptualization, Funding acquisition, Project administration, Writing – review & editing

  Affiliation The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom

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• James L. N. Wood,

  Roles Funding acquisition, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0002-0258-3188

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• Duncan J. Maskell,

  Roles Conceptualization, Funding acquisition, Writing – review & editing

  Affiliation The University of Melbourne, Victoria Australia

  https://orcid.org/0000-0002-5065-653X

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• Andrew J. Grant ,

  Contributed equally to this work with: Andrew J. Grant, Mark A. Holmes

  Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Writing – original draft, Writing – review & editing

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0001-9746-2989

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•  [ ... ],
• Mark A. Holmes

  Contributed equally to this work with: Andrew J. Grant, Mark A. Holmes

  Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: mah1@cam.ac.uk

  Affiliation Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

  https://orcid.org/0000-0002-5454-1625

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