This is the RSV phylogenetic analysis workflow which excludes G from tree building steps. It is based on the Nextstrain/RSV workflow.
Input metadata and sequences for RSV-A and RSV-B are available on data.nextstrain.org
These data are generously shared by labs around the world and deposited in NCBI genbank by the authors. Please contact these labs first if you plan to publish using these data.
The workflow produces whole genome trees for RSV-A and RSV-B, with the highly variable G gene excluded from tree building steps.
To run the workflow, use ``snakemake -j4 -p --configfile config/configfile.yaml ` and nextstrain view auspice to visualise results.
Follow the standard installation instructions for Nextstrain's suite of software tools.
We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances.