README.md

Beestat

Accompanying repository for association between viral loads and bee colony health in Belgium.

generate figures

All source data can be found under the 'data' folder. To generate the figures, first clone the repository and create the conda environment:

git clone git@github.com:Matthijnssenslab/Beestat.git
cd Beestat
conda env create -f conda.yaml -n beestat

or if you have mamba

mamba env create -f conda.yaml -n beestat

and run

conda activate beestat
snakemake --cores 1 -s generate_figures.smk

If you have multiple threads available you can up the number of cores (though the entire workflow shouldn't take longer then a couple of minutes on a regular pc). The figures will be generated inside the 'output' folder, some dataframes will be generated inside the 'data' folder, prefixed with 'out_'.

data

• gadm41_BEL_4.json

geojson file for Belgium, downloaded from gadm

• metadata.tsv

contains spatial information (on commune level) for all samples.

• metagenomic_coverage.tsv

normalised coverage for all included viruses, as assayed in our metagenomic study

• qpcr_abs.tsv

Absolute quantification values (by qRT-PCR) for all seven included viruses.

• sequences.fasta

Raw (nucleotide) sequences for all seven viruses.

• trees/*

Different phylogenetic trees as inferred by iqtree (plotted in figure 1).