augur builds for seattle flu study

This is the (in development) augur build for understanding influenza dynamics in Seattle. It is based off this nextstrain build.

Reassortment

Aim

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.

Method

In development.

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

Running

This build starts by pulling sequences from our live fauna database (a RethinkDB instance). This requires environment variables FAUNA_PATH, RETHINK_HOST and RETHINK_AUTH_KEY to be set.

snakemake