Publication by: Johannes Hahmann, Arjuna Selvakumar, Boris N. Schüpp, Montgomery Labudda, Yuanxu Zhou, Gurudas Chakraborty, Frauke Gräter, and Andreas Herrmann
Download by using
git clone https://github.com/graeter-group/DNAHairpins
in the desired directory.
The software runs on a standard computer with a sufficient amount of RAM. The Next Generation Sequencing code runs for the major dataset in less then 5 minutes.
Next Generation Sequencing: Software will run in a common python3 enviroment (tested with Python 3.13).
Required python packages: matplotlib, seaborn, numpy, scipy
Molecular Dynamics: Software can be run in a Linux terminal (only code with .sh) with GROMACS (tested on version 2025.2) and python3 installed.
Any other code (.py) runs with in a common python3 enviroment (tested with Python 3.13).
Required python packages: matplotlib, seaborn, pandas, numpy, scipy
Here, a full analysis pipeline for NGS data (.fastq) is provided. The raw data can be downloaded from Zenodo. NGSFilteringAlgorithm.py performs the analysis of NGS data based on a custom config file provided in the RunConfigurations directory. Additionally, all further analysis of sequencing data and the creation of plots are available in DistributionAnalysisHairpins.py, DistributionAnalysisNickedDNA.py, PlottingHairpins.py, and PlottingHairpinsSelfAssembly.py.
Here, the full code to set up the simulations on an HPC environment is provided. In SimulationSetup/, the PDB files and required input files are located. In DataExtraction/, the scripts for processing trajectories are found. The raw trajectory data can be obtained from Zenodo. Additionally, in Analysis/, the Python code for further analysis of end-to-end distances and bond forces, as well as the code for visualization, is provided.
For any questions regarding the provided software please contact Boris N. Schüpp (boris.schuepp@mtl.maxplanckschools.de).