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@article{Faria2017,
doi = {10.1038/nature22401},
url = {https://doi.org/10.1038/nature22401},
year = {2017},
month = {may},
publisher = {Springer Nature},
volume = {546},
number = {7658},
pages = {406--410},
author = {N. R. Faria and J. Quick and I.M. Claro and J. Th{\'{e}}z{\'{e}} and J. G. de Jesus and M. Giovanetti and M. U. G. Kraemer and S. C. Hill and A. Black and A. C. da Costa and L. C. Franco and S. P. Silva and C.-H. Wu and J. Raghwani and S. Cauchemez and L. du Plessis and M. P. Verotti and W. K. de Oliveira and E. H. Carmo and G. E. Coelho and A. C. F. S. Santelli and L. C. Vinhal and C. M. Henriques and J. T. Simpson and M. Loose and K. G. Andersen and N. D. Grubaugh and S. Somasekar and C. Y. Chiu and J. E. Mu{\~{n}}oz-Medina and C. R. Gonzalez-Bonilla and C. F. Arias and L. L. Lewis-Ximenez and S. A. Baylis and A. O. Chieppe and S. F. Aguiar and C. A. Fernandes and P. S. Lemos and B. L. S. Nascimento and H. A. O. Monteiro and I. C. Siqueira and M. G. de Queiroz and T. R. de Souza and J. F. Bezerra and M. R. Lemos and G. F. Pereira and D. Loudal and L. C. Moura and R. Dhalia and R. F. Fran{\c{c}}a and T. Magalh{\~{a}}es and E. T. Marques and T. Jaenisch and G. L. Wallau and M. C. de Lima and V. Nascimento and E. M. de Cerqueira and M. M. de Lima and D. L. Mascarenhas and J. P. Moura Neto and A. S. Levin and T. R. Tozetto-Mendoza and S. N. Fonseca and M. C. Mendes-Correa and F. P. Milagres and A. Segurado and E. C. Holmes and A. Rambaut and T. Bedford and M. R. T. Nunes and E. C. Sabino and L. C. J. Alcantara and N. J. Loman and O. G. Pybus},
title = {Establishment and cryptic transmission of Zika virus in Brazil and the Americas},
journal = {Nature}
}
@article{Quick2015,
doi = {10.1186/s13059-015-0677-2},
url = {https://doi.org/10.1186/s13059-015-0677-2},
year = {2015},
month = {may},
publisher = {Springer Nature},
volume = {16},
number = {1},
author = {Joshua Quick and Philip Ashton and Szymon Calus and Carole Chatt and Savita Gossain and Jeremy Hawker and Satheesh Nair and Keith Neal and Kathy Nye and Tansy Peters and Elizabeth De Pinna and Esther Robinson and Keith Struthers and Mark Webber and Andrew Catto and Timothy J. Dallman and Peter Hawkey and Nicholas J. Loman},
title = {Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella},
journal = {Genome Biology}
}
@article{Votintseva2017,
doi = {10.1128/jcm.02483-16},
url = {https://doi.org/10.1128/jcm.02483-16},
year = {2017},
month = {mar},
publisher = {American Society for Microbiology},
volume = {55},
number = {5},
pages = {1285--1298},
author = {Antonina A. Votintseva and Phelim Bradley and Louise Pankhurst and Carlos del Ojo Elias and Matthew Loose and Kayzad Nilgiriwala and Anirvan Chatterjee and E. Grace Smith and Nicolas Sanderson and Timothy M. Walker and Marcus R. Morgan and David H. Wyllie and A. Sarah Walker and Tim E. A. Peto and Derrick W. Crook and Zamin Iqbal},
editor = {Yi-Wei Tang},
title = {Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples},
journal = {Journal of Clinical Microbiology}
}
@article{Gardy2017,
doi = {10.1038/nrg.2017.88},
url = {https://doi.org/10.1038/nrg.2017.88},
year = {2017},
month = {nov},
publisher = {Springer Nature},
volume = {19},
number = {1},
pages = {9--20},
author = {Jennifer L. Gardy and Nicholas J. Loman},
title = {Towards a genomics-informed, real-time, global pathogen surveillance system},
journal = {Nature Reviews Genetics}
}
@article{Koren2017,
doi = {10.1101/gr.215087.116},
url = {https://doi.org/10.1101/gr.215087.116},
year = {2017},
month = {mar},
publisher = {Cold Spring Harbor Laboratory},
volume = {27},
number = {5},
pages = {722--736},
author = {Sergey Koren and Brian P. Walenz and Konstantin Berlin and Jason R. Miller and Nicholas H. Bergman and Adam M. Phillippy},
title = {Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation},
journal = {Genome Research}
}