Snakemake workflow: GENQC

A Snakemake-based tool for quality control of synthetic oligonucleotide sequencing data produced by ONT sequencers, developed for Ubuntu.

Installation

For not bioinformaticians

1. On the right side you should find Release window and open it by clicking "Releases"
   

2. Once you open window, at the very top you will see latest release version. Press on installer.sh to download it. Download it into folder where you want to install our tool. If you download script and install into "Downloads" folder, after cleaning "Downloads" you may cry a lot.
   

3. With right click open properties of downloaded file.
   

4. Go to "Permissions" and make sure "Allow executing file as program" is pressed. You can close a window.
   

5. With right of click on the same file press "Run as program"
   

6. Enter password from current user and Press Enter. You will NOT see the entered symbols
   

7. If installation is successful, you will see oligo-bench folder with all required content inside. Otherwise create Issue in tab "Issues" on GitHub.

For bioinformaticians

1. Install miniconda, if you do not have it.
2. Download and unzip project.
3. Go inside project

cd oligo-bench-main

4. Create conda environment

conda create -c conda-forge -c bioconda -p ./oligo snakemake minimap2 last samtools pandas snakefmt pysam plotly PyYAML requests -y

5. If you prefer to have possibility to run UI, install PyQt6

conda activate -p ./oligo
pip install PyQt6

Running

For not bioinformaticians

1. Open "oligo-bench" folder to see all the files.
2. With right click on UI.sh press "Run as program"

For bioinformaticians

1. Activate environment

conda activate -p ./oligo

2. Run script

./run.sh