pakPy

This project is part of the FORZA subproject of Dr. Kogge's Computer Lab in the University of Notre Dame Department of Computer Science and Engineering

Inspired by the original work of Dr. P Ghosh et al. in the PaKman: A Scalable Algorithm for Generating Genomic Contigs on Distributed Memory Machines (github). This project works to speed up the outcomes seen in the paper.

Dependencies

This code is currently set to only run on Python 3.11.0. To change this, please change the version in the .python-version document. The following Python libraries must be installed for the code to run.

Library	Install
networkx	pip install networkx
numpy	pip install numpy
keras	pip install keras
pandas	pip install pandas
scikit-learn	pip install scikit-learn
scipy	pip install scipy
tensorflow	pip install tensorflow
matplotlib	pip install matplotlib

Running code

Enter in the command line

./run.sh

To compile code into ASM use GCC

gcc -c graph.S -o graph.o

gcc graph.o -o graph

gcc -S graph.c -o graph.s

gcc -c graph.s

Verified Platforms

The following code has be tested on these platforms

MacOS	Debuain/Ubuntu	GNU/Linux