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@ARTICLE{Zerbino2008-kh,
  title       = "Velvet: algorithms for de novo short read assembly using de
                 Bruijn graphs",
  author      = "Zerbino, Daniel R and Birney, Ewan",
  affiliation = "EMBL-European Bioinformatics Institute, Wellcome Trust Genome
                 Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.",
  journal     = "Genome Res.",
  volume      =  18,
  number      =  5,
  pages       = "821--829",
  month       =  may,
  year        =  2008,
  language    = "en"
}

@ARTICLE{Zerbino2009-pt,
  title       = "Pebble and rock band: heuristic resolution of repeats and
                 scaffolding in the velvet short-read de novo assembler",
  author      = "Zerbino, Daniel R and McEwen, Gayle K and Margulies, Elliott H
                 and Birney, Ewan",
  affiliation = "European Bioinformatics Institute, Wellcome Trust Genome
                 Campus, Hinxton, Cambridge, UK. zerbino@ebi.ac.uk",
  journal     = "PLoS One",
  volume      =  4,
  number      =  12,
  pages       = "e8407",
  month       =  "22~" # dec,
  year        =  2009,
  language    = "en"
}

@ARTICLE{Chewapreecha2014-on,
  title       = "Dense genomic sampling identifies highways of pneumococcal
                 recombination",
  author      = "Chewapreecha, Claire and Harris, Simon R and Croucher,
                 Nicholas J and Turner, Claudia and Marttinen, Pekka and Cheng,
                 Lu and Pessia, Alberto and Aanensen, David M and Mather,
                 Alison E and Page, Andrew J and Salter, Susannah J and Harris,
                 David and Nosten, Francois and Goldblatt, David and Corander,
                 Jukka and Parkhill, Julian and Turner, Paul and Bentley,
                 Stephen D",
  affiliation = "The Wellcome Trust Sanger Institute, Wellcome Trust Genome
                 Campus, Hinxton, Cambridge, CB10 1SA, UK. Department of
                 Infectious Disease Epidemiology, Imperial College London, St.
                 Mary's Hospital, London, W2 1PG, UK. Shoklo Malaria Research
                 Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty
                 of Tropical Medicine, Mahidol University, Maesot 63110,
                 Thailand. Cambodia-Oxford Medical Research Unit, Angkor
                 Hospital for Children, Siem Reap, Cambodia. Centre for
                 Tropical Medicine, Nuffield Department of Medicine, University
                 of Oxford, Oxford, OX3 7LJ, UK. Helsinki Institute for
                 Information Technology HIIT, Department of Information and
                 Computer Science, Aalto University, 00076, Finland. Department
                 of Mathematics and Statistics, University of Helsinki, 00014,
                 Finland. Immunobiology Unit, Institute of Child Health,
                 University College London, WC1N 1EH, UK. Department of
                 Medicine, University of Cambridge, Addenbrooke's Hospital,
                 Cambridge, CB2 0QQ, UK.",
  journal     = "Nat. Genet.",
  volume      =  46,
  number      =  3,
  pages       = "305--309",
  month       =  mar,
  year        =  2014,
  language    = "en"
}

@ARTICLE{Wong2015-fl,
  title       = "Phylogeographical analysis of the dominant multidrug-resistant
                 {H58} clade of Salmonella Typhi identifies inter- and
                 intracontinental transmission events",
  author      = "Wong, Vanessa K and Baker, Stephen and Pickard, Derek J and
                 Parkhill, Julian and Page, Andrew J and Feasey, Nicholas A and
                 Kingsley, Robert A and Thomson, Nicholas R and Keane,
                 Jacqueline A and Weill, Fran{\c c}ois-Xavier and Edwards,
                 David J and Hawkey, Jane and Harris, Simon R and Mather,
                 Alison E and Cain, Amy K and Hadfield, James and Hart, Peter J
                 and Thieu, Nga Tran Vu and Klemm, Elizabeth J and Glinos,
                 Dafni A and Breiman, Robert F and Watson, Conall H and
                 Kariuki, Samuel and Gordon, Melita A and Heyderman, Robert S
                 and Okoro, Chinyere and Jacobs, Jan and Lunguya, Octavie and
                 Edmunds, W John and Msefula, Chisomo and Chabalgoity, Jose A
                 and Kama, Mike and Jenkins, Kylie and Dutta, Shanta and Marks,
                 Florian and Campos, Josefina and Thompson, Corinne and Obaro,
                 Stephen and MacLennan, Calman A and Dolecek, Christiane and
                 Keddy, Karen H and Smith, Anthony M and Parry, Christopher M
                 and Karkey, Abhilasha and Mulholland, E Kim and Campbell,
                 James I and Dongol, Sabina and Basnyat, Buddha and Dufour,
                 Muriel and Bandaranayake, Don and Naseri, Take Toleafoa and
                 Singh, Shalini Pravin and Hatta, Mochammad and Newton, Paul
                 and Onsare, Robert S and Isaia, Lupeoletalalei and Dance,
                 David and Davong, Viengmon and Thwaites, Guy and Wijedoru,
                 Lalith and Crump, John A and De Pinna, Elizabeth and Nair,
                 Satheesh and Nilles, Eric J and Thanh, Duy Pham and Turner,
                 Paul and Soeng, Sona and Valcanis, Mary and Powling, Joan and
                 Dimovski, Karolina and Hogg, Geoff and Farrar, Jeremy and
                 Holt, Kathryn E and Dougan, Gordon",
  affiliation = "1] Wellcome Trust Sanger Institute, Hinxton, UK. [2]
                 Department of Microbiology, Addenbrooke's Hospital, Cambridge
                 University Hospitals National Health Service (NHS) Foundation
                 Trust, Cambridge, UK. 1] Hospital for Tropical Diseases,
                 Wellcome Trust Major Overseas Programme, Oxford University
                 Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre
                 for Tropical Medicine and Global Health, Nuffield Department
                 of Clinical Medicine, Oxford University, Oxford, UK. [3]
                 Department of Infectious and Tropical Diseases, London School
                 of Hygiene and Tropical Medicine, London, UK. Wellcome Trust
                 Sanger Institute, Hinxton, UK. Liverpool School of Tropical
                 Medicine, Liverpool, UK. 1] Wellcome Trust Sanger Institute,
                 Hinxton, UK. [2] Institute of Food Research, Norwich Research
                 Park, Norwich, UK. 1] Wellcome Trust Sanger Institute,
                 Hinxton, UK. [2] Department of Infectious and Tropical
                 Diseases, London School of Hygiene and Tropical Medicine,
                 London, UK. Institut Pasteur, Unit{\'e} des Bact{\'e}ries
                 Pathog{\`e}nes Ent{\'e}riques, Paris, France. Department of
                 Biochemistry and Molecular Biology, Bio21 Molecular Science
                 and Biotechnology Institute, University of Melbourne,
                 Melbourne, Victoria, Australia. 1] Department of Biochemistry
                 and Molecular Biology, Bio21 Molecular Science and
                 Biotechnology Institute, University of Melbourne, Melbourne,
                 Victoria, Australia. [2] Faculty of Veterinary and
                 Agricultural Sciences, University of Melbourne, Melbourne,
                 Victoria, Australia. Institute of Biomedical Research, School
                 of Immunity and Infection, College of Medicine and Dental
                 Sciences, University of Birmingham, Birmingham, UK. Hospital
                 for Tropical Diseases, Wellcome Trust Major Overseas
                 Programme, Oxford University Clinical Research Unit, Ho Chi
                 Minh City, Vietnam. 1] Kenya Medical Research Institute
                 (KEMRI), Nairobi, Kenya. [2] Centers for Disease Control and
                 Prevention, Atlanta, Georgia, USA. [3] Emory Global Health
                 Institute, Atlanta, Georgia, USA. Centre for the Mathematical
                 Modelling of Infectious Diseases, Department of Infectious
                 Disease Epidemiology, London School of Hygiene and Tropical
                 Medicine, London, UK. 1] Wellcome Trust Sanger Institute,
                 Hinxton, UK. [2] Kenya Medical Research Institute (KEMRI),
                 Nairobi, Kenya. Institute of Infection and Global Health,
                 University of Liverpool, Liverpool, UK. Malawi-Liverpool
                 Wellcome Trust Clinical Research Programme, College of
                 Medicine, University of Malawi, Blantyre, Malawi. 1]
                 Department of Clinical Sciences, Institute of Tropical
                 Medicine, Antwerp, Belgium. [2] Department of Microbiology and
                 Immunology, Katholieke Universiteit (KU) Leuven, University of
                 Leuven, Leuven, Belgium. 1] National Institute for Biomedical
                 Research, Kinshasa, Democratic Republic of the Congo. [2]
                 University Hospital of Kinshasa, Kinshasa, Democratic Republic
                 of the Congo. 1] Malawi-Liverpool Wellcome Trust Clinical
                 Research Programme, College of Medicine, University of Malawi,
                 Blantyre, Malawi. [2] Microbiology Department, College of
                 Medicine, University of Malawi, Blantyre, Malawi. Departamento
                 de Desarrollo Biotecnol{\'o}gico, Instituto de Higiene,
                 Facultad de Medicina, Montevideo, Uruguay. Ministry of Health,
                 Suva, Fiji. Fiji Health Sector Support Program, Suva, Fiji.
                 National Institute of Cholera and Enteric Diseases, Kolkata,
                 India. International Vaccine Institute, Department of
                 Epidemiology, Seoul, Republic of Korea. Enteropathogen
                 Division, Administraci{\'o}n Nacional de Laboratorios e
                 Institutos de Salud (ANLIS) Carlos G. Malbran Institute,
                 Buenos Aires, Argentina. 1] Hospital for Tropical Diseases,
                 Wellcome Trust Major Overseas Programme, Oxford University
                 Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre
                 for Tropical Medicine and Global Health, Nuffield Department
                 of Clinical Medicine, Oxford University, Oxford, UK. 1]
                 Division of Pediatric Infectious Diseases, University of
                 Nebraska Medical Center, Omaha, Nebraska, USA. [2] University
                 of Abuja Teaching Hospital, Abuja, Nigeria. [3] Bingham
                 University, Karu, Nigeria. 1] Wellcome Trust Sanger Institute,
                 Hinxton, UK. [2] Institute of Biomedical Research, School of
                 Immunity and Infection, College of Medicine and Dental
                 Sciences, University of Birmingham, Birmingham, UK. [3]
                 Novartis Vaccines Institute for Global Health, Siena, Italy.
                 Centre for Tropical Medicine and Global Health, Nuffield
                 Department of Clinical Medicine, Oxford University, Oxford,
                 UK. Centre for Enteric Diseases, National Institute for
                 Communicable Diseases, Division in the National Health
                 Laboratory Service, University of the Witwatersrand,
                 Johannesburg, South Africa. 1] Department of Clinical
                 Research, London School of Hygiene and Tropical Medicine,
                 London, UK. [2] Graduate School of Tropical Medicine and
                 Global Health, Nagasaki University, Nagasaki, Japan. Patan
                 Academy of Health Sciences, Wellcome Trust Major Overseas
                 Programme, Oxford University Clinical Research Unit,
                 Kathmandu, Nepal. 1] Department of Infectious and Tropical
                 Diseases, London School of Hygiene and Tropical Medicine,
                 London, UK. [2] Murdoch Childrens Research Institute,
                 Melbourne, Victoria, Australia. Enteric and Leptospira
                 Reference Laboratory, Institute of Environmental Science and
                 Research, Ltd. (ESR), Porirua, New Zealand. National Centre
                 for Biosecurity and Infectious Disease, Institute of
                 Environmental Science and Research, Porirua, New Zealand.
                 Samoa Ministry of Health, Apia, Samoa. National Influenza
                 Center, World Health Organization, Center for Communicable
                 Disease Control, Suva, Fiji. Department of Microbiology,
                 Hasanuddin University, Makassar, Indonesia. 1] Centre for
                 Tropical Medicine and Global Health, Nuffield Department of
                 Clinical Medicine, Oxford University, Oxford, UK. [2] Lao
                 Oxford Mahosot Wellcome Trust Research Unit, Microbiology
                 Laboratory, Mahosot Hospital, Vientiane, Laos. Kenya Medical
                 Research Institute (KEMRI), Nairobi, Kenya. National Health
                 Services, Tupua Tamasese Meaole Hospital, Apia, Samoa. Lao
                 Oxford Mahosot Wellcome Trust Research Unit, Microbiology
                 Laboratory, Mahosot Hospital, Vientiane, Laos. 1]
                 Mahidol-Oxford Tropical Medicine Research Unit, Faculty of
                 Tropical Medicine, Mahidol University, Bangkok, Thailand. [2]
                 Paediatric Emergency Medicine, Chelsea and Westminster
                 Hospital, London, UK. Centre for International Health and
                 Otago International Health Research Network, Dunedin School of
                 Medicine, University of Otago, Dunedin, New Zealand.
                 Salmonella Reference Service, Public Health England,
                 Colindale, London, UK. Emerging Disease Surveillance and
                 Response, Division of Pacific Technical Support, World Health
                 Organization, Suva, Fiji. 1] Centre for Tropical Medicine and
                 Global Health, Nuffield Department of Clinical Medicine,
                 Oxford University, Oxford, UK. [2] Mahidol-Oxford Tropical
                 Medicine Research Unit, Faculty of Tropical Medicine, Mahidol
                 University, Bangkok, Thailand. [3] Cambodia-Oxford Medical
                 Research Unit, Angkor Hospital for Children, Siem Reap,
                 Cambodia. Cambodia-Oxford Medical Research Unit, Angkor
                 Hospital for Children, Siem Reap, Cambodia. Microbiological
                 Diagnostic Unit-Public Health Laboratory, Department of
                 Microbiology and Immunology at the Peter Doherty Institute for
                 Infection and Immunity, University of Melbourne, Melbourne,
                 Victoria, Australia.",
  journal     = "Nat. Genet.",
  volume      =  47,
  number      =  6,
  pages       = "632--639",
  month       =  jun,
  year        =  2015,
  language    = "en"
}

@ARTICLE{Page2016-zp,
  title       = "Robust high-throughput prokaryote de novo assembly and
                 improvement pipeline for Illumina data",
  author      = "Page, Andrew J and De Silva, Nishadi and Hunt, Martin and
                 Quail, Michael A and Parkhill, Julian and Harris, Simon R and
                 Otto, Thomas D and Keane, Jacqueline A",
  affiliation = "Pathogen Informatics, Wellcome Trust Sanger Institute ,
                 Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire ,
                 UK. Biochemical Development, Wellcome Trust Sanger Institute ,
                 Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire ,
                 UK. Pathogen Genomics, Wellcome Trust Sanger Institute ,
                 Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire ,
                 UK. Parasite Genomics, Wellcome Trust Sanger Institute ,
                 Wellcome Genome Campus, Hinxton, CB10 1SA, Cambridgeshire ,
                 UK.",
  journal     = "Microb Genom",
  volume      =  2,
  number      =  8,
  pages       = "e000083",
  month       =  aug,
  year        =  2016,
  keywords    = "assembly; high-throughput; illumina; prokaryotic",
  language    = "en"
}
