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the (in development) augur build for understanding influenza dynamics in Seattle
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analyses Record clade and date of introductions Oct 14, 2019
config
scripts Small update to augur build Oct 6, 2019
source-data add more vaccination data, export age and vaccination coverage scores Dec 30, 2018
.gitignore Update closest genomic neighbor plotting Oct 3, 2019
.pylintrc Define clusters based on connected components Jun 15, 2019
.travis.yml
README.md
Snakefile Update clade definitions Oct 13, 2019
batch.py
calculating_fst_per_category.py changing all instances of region to category for generalizability Aug 1, 2019
requirements.txt

README.md

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
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