tkmanabat / sars-cov-2-clade-identifier

SARS-CoV-2 Clade identifier with SNP data using machine learning.

SARS-CoV-2-Clade-Identifier

Background and Objective 📰

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:

Code Organization 🤹‍♂️

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.

Setup 💻

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