Genome Toolkit

Genome Toolkit is a small Python bioinformatics toolkit for working with DNA sequences and learning how common bioinformatics algorithms work.

Current capabilities

• Represent and validate DNA sequences
• Load sequences from plain-text files
• Read FASTA files
• Select FASTA sequences by identifier or index
• Count occurrences of a k-mer
• Find the most frequent k-mers in a DNA sequence

Requirements

The project uses uv for Python, dependency, and virtual-environment management.

Install uv

Linux

curl -LsSf https://astral.sh/uv/install.sh | sh

macOS

curl -LsSf https://astral.sh/uv/install.sh | sh

Windows

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Verify the installation:

uv --version

Installation

Clone the repository:

git clone https://github.com/rebelC0der/Genome_Toolkit.git
cd Genome_Toolkit

Synchronize the environment:

uv sync

uv creates and manages the project's virtual environment automatically.

Running Genome Toolkit

Run the development application:

uv run application.py

Run the complete tests:

uv run pytest -v

Repository

Genome Toolkit is developed as an educational bioinformatics project focused on simple, readable implementations of biological data handling and algorithms.