Nathaniel L. Matteson 1
1 Department of Immunology and Microbiology, Scripps Research, La Jolla, United States
Repository describes the analysis pipeline used for my ongoing analysis of West Nile virus in the United States. Primarily we're interested in the environmental, ecological, and viral factors that drive intermittent seasonal outbreaks.
The primary analysis pipeline is provided as a snakemake pipeline in the workflow directory.
Additional details there describe the pipeline in greater depth.
Input files for the pipeline, representing an up-to-date alignment and metadata, are present in the input directory.
Additional files and data, either generated by the pipeline or necessary for analyses, are provided in the data folder.
Though some files may not be present at the moment due to unclear licenses.
Complete analyses and figures are in the analysis directory.
Please note that this data is released as work in progress by the WestNile 4K Project 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.