This repo contains code and communications related to a class project for PLNTPTH 6193 - Practical Computing for biologists
A study by De Angelis et al. found associations between the human gut microbiome and diet. In it they took shotgun metagenomic samples of the human gut microbiome from 30 volunteers on either a omnivourus, vegan, or vegetarian diet and correlated diet with gut microbial profile.
The human gut microbiome shotgun metagenomic data with sequences filtered for human reads and trimmed of low-quality bases are publically available through the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA; SRP083099, Bioproject ID PRJNA340216).
In my project I intend to
The workflow for this analysis is all self contained in the __runner_script.sh, which itself relies on multiple SLURM batch job scripts located in the scripts__ directory
Overall, the workflow is
fastqcKraken2 (needs databases)BrackenKraken2BrackenFollowing the runner script is simple, but time consuming as each batch job can take several hours to days (downloading metagenomics data takes quite some time)
All directories, conda enviroments, and outputs are autopopulated by running the script making this code easy to run and reporducable
This script is customized for this specific data analysis - this code could be used to check other NCBI metagenomic datasets, but could not be run as is for say your own custom data
What this script is missing is quality improvement and host read removal which would be done with something like trimmomatic and BowTie2 respectivly - since the NCBI data has already had these steps completed, they were not included in this workflow.
Most of this code works for me, but I have had particular trouble getting the get_data.sh script to download all the files and it may only partially download the requested data (as in not all of the requested files, the files that are available are complete though). I have used what data did download for this project, and have not tried to rerun it due to the large time requirments. These scripts were able to run on the data available and should still work with new files though.
Additionally, the file paths for all of the scripts require the user to have acess to the /fs/ess/PAS2700/users/$USER directory. All of the scripts currently require that this path be available, and other users will need to tweak the scripts to be able to use another directory, available at the top of each script.