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BarCoder Toolkit: The Pinnacle of Genomic Experimentation

Unlock the full potential of genome-scale experiments with the BarCoder Toolkit, a state-of-the-art suite designed for peak performance, precision, and adaptability. This toolkit is the epitome of cutting-edge genomic data processing, offering an array of utilities from sequence alignment to data compression and read analysis, all while adhering to the SOLID principles for extreme interoperability and dependency injection.

Installation

Conda/Mamba

Set up the BarCoder environment with ease using Conda or Mamba:

  1. Streamlined Dependencies: The environment.yml file includes all necessary dependencies, such as Bowtie, for a hassle-free setup.

  2. Environment Setup:

    • With Mamba: 
      mamba env create -f environment.yml
    • With Conda: 
      conda env create -f environment.yml

  3. Ready to Go: Post-installation, dive into the toolkit's functionalities. Our classes are crafted to output JSON for valid genomic matches, streamlining downstream analysis and integration.

Pipenv (For Development)

For developers, Pipenv provides a seamless dependency management experience:

  • Note: Bowtie is not included in the Pipenv environment and should be managed separately.
  • Setup: 
    pipenv install --dev

Evolving with Precision

The BarCoder Toolkit is in constant evolution, embracing more sophisticated data structures and seamless integration with a plethora of bioinformatics tools. Stay tuned for our latest updates and enhancements that push the boundaries of genomic research.

Contributing

We invite you to contribute to the BarCoder Toolkit's journey towards excellence. Your expertise can help shape the future of genomic experimentation. Engage with us through the project's issue tracker for bug reports, feature proposals, or pull requests.