augur builds for seattle flu study
Given phylogenies for each segement, we aim to identify sets of tips which have not undergone reassortment. This allows the concatenation of the segments for each set of (non-reassorting) tips, allowing the construction of a more informative phylogeny.
The easiest way to rerun the algorithm when the script has changed is to run:
snakemake --force results/reassort_h3n2_2y_5vpm.json && snakemake snakemake --force results/reassort_h3n2_2y_20vpm.json && snakemake
This build starts by pulling sequences from our live fauna database (a RethinkDB instance).
This requires environment variables
RETHINK_AUTH_KEY to be set.