Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

Author:

Wymant Chris12ORCID,Blanquart François2,Golubchik Tanya13,Gall Astrid45,Bakker Margreet6,Bezemer Daniela7,Croucher Nicholas J2,Hall Matthew12,Hillebregt Mariska7,Ong Swee Hoe5ORCID,Ratmann Oliver28,Albert Jan910,Bannert Norbert11,Fellay Jacques1213,Fransen Katrien14,Gourlay Annabelle1516,Grabowski M Kate17,Gunsenheimer-Bartmeyer Barbara18,Günthard Huldrych F1920,Kivelä Pia21,Kouyos Roger1920,Laeyendecker Oliver22,Liitsola Kirsi21,Meyer Laurence23,Porter Kholoud15,Ristola Matti21,van Sighem Ard7,Berkhout Ben6ORCID,Cornelissen Marion6,Kellam Paul2425,Reiss Peter726,Fraser Christophe12ORCID,

Affiliation:

1. Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK

2. Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, UK

3. Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK

4. Department of Veterinary Medicine, University of Cambridge, Cambridge, UK

5. Virus Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK

6. Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands

7. Stichting HIV Monitoring, Amsterdam, The Netherlands

8. Department of Mathematics, Imperial College London, London, UK

9. Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden

10. Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden

11. Division for HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany

12. School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

13. Swiss Institute of Bioinformatics, Lausanne, Switzerland

14. HIV/STI Reference Laboratory, Department of Clinical Science, WHO Collaborating Centre, Institute of Tropical Medicine, Antwerpen, Belgium

15. Institute for Global Health, University College London, London, UK

16. Department of Population Health, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK

17. Department of Pathology, John Hopkins University, Baltimore, MD, USA

18. Department of Infectious Disease Epidemiology, Robert Koch-Institute, Berlin, Germany

19. Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland

20. Institute of Medical Virology, University of Zurich, Zurich, Switzerland

21. Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland

22. Division of Intramural Research, NIAID, NIH, Baltimore, MD, USA

23. INSERM CESP U1018, Université Paris Sud, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France

24. Kymab Ltd, Cambridge, UK

25. Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK

26. Department of Global Health, Academic Medical Center and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands

Funder

H2020 European Research Council

Publisher

Oxford University Press (OUP)

Subject

Virology,Microbiology

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