This is a project that serves as an example of documenting your workflows during bioinformatical research. Personally, I made a little GoogleDoc with the work notes from the four days of the course. The overall goal is to analyze the interplay of T5 bacteriophage and its host - how the virus circumvents the restriction-modification system employing various approaches and the bacteria tries to counter them using, for example, the PARIS system. To this end we study raw phage genome reads, pre-process them and perform variant calling using the industry-standart tools.
This project has three branches:
- Main/master branch with the description, enviroment configuration and barren of anything else. Please use conda and enter
conda env create -f envs/environment.yml- it has everything necessary for both approaches. - Bash branch where automation is achieved using core bash script functionality.
- Snakemake branch which employs snakemake pipeline management package for the same processes.
Hit the author up at my twitter.