This is the code repository for SARS-CoV-2 clade identifier with Single Nucleotide Polymorphisms (SNPs) data using machine learning. A project of the Philippine Genome Center's 2021 Internship Program.
General Objective: Use Machine Learning to determine the Clades using SNPs of a given SARS-CoV-2 given sequence.
Specific Objectives:
- Use Machine Learning as another lens to understand SARS-CoV-2.
- Provide an alternative way for identifying clades.
- Proof of concept for future studies.
Project Workflow:
This repository is divided into five parts:
- Dataset Gathering/: contains steps on how SARS-CoV-2 sequences was collected/downloaded.
- Variant Calling Workflow/: contains information on was processing done to get the SNPs from the sequences.
- Clade Assignment/: contains steps on how clade assignment and processing was done.
- Concatenation and Data Preprocessing/: contains the notebook for concatenating the SNPs from the variant calling workflow and the clade from the clade assignment workflow.
- Machine Learning/: contains the machine learning models trained for this projects.
To get started:
- Clone the repository
git clone https://github.com/tkmanabat/SARS-CoV-2-Clade-Identifier.git
- In order that to run the notebooks, all dependencies must be installed. We provided a list of dependencies in
requirements.txt
pip install -r requirements.txt
- To open with Jupyter Notebook
jupyter notebook