Nextstrain data, pipelines, and visualizations for novel pathogen outbreak as part of ARTIC-network live workshop
Once you've run the pipeline, you can push the builds to artic-live/auspice so that they can be viewed via Nextstrain community builds feature.
This github has this folder populated already so that one doesn't have to run the pipelines.
Currently these builds still has the case labelled case128, and case numbers are nonsensical.
You can run two different 'types' of builds with this repository:
background-buildwill build S and L segment builds, with the primary case - one Snakefile can run both.cluster-buildswill build 3 different subsamples of the outbreak - initial cases, then with the additional 2, then with all of the outbreak cases - one Snakefile can run all 3
See each snakefile in each folder for instructions/details.
Background for L segment, with case
Background for S segment, with case