genome evolution experiment analysis

This pipeline can be used for the genomic analysis of evolution experiments, in which a population is sequenced multiple times over the course of the experiment.

Example run command for local execution:

snakemake --profile local --configfile test_data/run_config.yml

Example run command for cluster execution:

snakemake --profile cluster --configfile test_data/run_config.yml

A description of the produced plots is provided in this note.

retrieving annotations

To also retrieve annotations, execute the pipeline with:

snakemake plot_all annotate_all --profile cluster --configfile test_data/run_config.yml

This will produce files in the annotations folder with extracted mutated positions (positions.csv), and extracted annotations for positions that fall inside of a feature (annotations_hit.csv) or extracted closest forward and reverse annotations for positions that fall outside of a feature (annotations_miss.csv).

This requires the presence of GenBank files with annotations, see input data preparation

Important

The pipeline was developed for snakemake v7. Version 8 might introduce breaking changes for which the pipeline was not tested.