This is a collaboration between the CDC Dengue Branch and the Yale School of Public Health. Our data can be visualized on our Nextstrain community build.
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The Zika virus samples were sequenced using our [PrimalSeq protocol] (https://www.nature.com/articles/nprot.2017.066) and consensus sequences were generated using [iVar] (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7).
Detailed methods can be found on our website: http://grubaughlab.com/open-science/amplicon-sequencing/
Some of our analyses were performed using the nextstrain (augur) pipeline. These results can be visualized using auspice, accessing the link below:
Disclaimer. Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments – we’ll buy beers for #ResearchParasites that spot flaws and faults in the data and come up with improvements!
Grubaugh Lab | Yale School of Public Health (YSPH) | https://grubaughlab.com/