Quadrupia

Quadrupia is a database of G-Quadruplex sequences from 108,449 organismal genomes across the Tree of Life. This repository contains scripts used for analysis of the G-Quadruplex data.

Paper: https://www.biorxiv.org/content/10.1101/2024.07.09.602008v1.full

Directories

• raw_data/ (Input data): Contains extracted G4 sequences. Please contact us for access.
• metadata/: Contains text files and tabular data with metadata such as taxonomic groups, ftp paths for download and other information associated with reference genomes.
• scripts/: Contains scripts used for downloading, parsing and pre-processing data.
• slurm/: Contains scripts used for running jobs on the cluster.
  • batch/: Bash scripts for submitting batch jobs to slurm.
  • files/: Text files containing command line arguments for slurm scripts in the slurm/batch/ directory.
  • prep/: Python scripts for generating text files in the slurm/files/ directory.
• data/: Contains extracted G4 sequences and GFF data in bed format for further processing, and is generated using scripts in the scripts/ and the slurm/ directories.
• results/: Contains results from processing of data in data/ using scripts in the scripts/ directory.
• notebooks/: Contains Jupyter notebooks that use the processed data in the results/ directory for further analysis and data visualization.
• supplementary_data/: Contains supplementary data for the paper.

Getting Started

To get started with the project, clone the repository and install the required dependencies. Optionally, create a new conda environment for the project.

# create a new conda environment (optional)
conda create -n quadrupia python=3.9
conda activate quadrupia

# clone repository and install dependencies
git clone https://github.com/Georgakopoulos-Soares-lab/Quadrupia.git
cd Quadrupia
pip install -r requirements.txt

Contact

For questions, or to report bugs, contact -

nmc6088@psu.edu (Nikol Chantzi)
abn5461@psu.edu (Akshatha Nayak)
izg5139@psu.edu (Ilias Georgakopoulos-Soares)